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PDBsum entry 1gix

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protein dna_rna links
Ribosome PDB id
1gix
Jmol PyMol
Contents
Protein chains
234 a.a.* *
206 a.a.* *
208 a.a.* *
150 a.a.* *
101 a.a.* *
155 a.a.* *
138 a.a.* *
127 a.a.* *
98 a.a.* *
119 a.a.* *
124 a.a.* *
125 a.a.* *
60 a.a.* *
88 a.a.* *
83 a.a.* *
104 a.a.* *
73 a.a.* *
80 a.a.* *
99 a.a.* *
24 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1gix
Name: Ribosome
Title: Crystal structure of the ribosome at 5.5 a resolution. This 1gix, contains the 30s ribosome subunit, three tRNA, and mr molecules. 50s ribosome subunit is in the file 1giy
Structure: 30s 16s ribosomal RNA. Chain: a. tRNA(phe). Chain: b, c. Engineered: yes. Other_details: a-site tRNA chain b, p-site tRNA chain c. tRNA(phe). Chain: d. Engineered: yes.
Source: Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Other_details: sequence naturally occurs in saccharomyces cerevisiae. Organism_taxid: 274
Biol. unit: 25mer (from PQS)
Resolution:
5.50Å     R-factor:   not given    
Authors: M.M.Yusupov,G.Z.Yusupova,A.Baucom,K.Lieberman,T.N.Earnest,J. H.F.Noller
Key ref:
M.M.Yusupov et al. (2001). Crystal structure of the ribosome at 5.5 A resolution. Science, 292, 883-896. PubMed id: 11283358 DOI: 10.1126/science.1060089
Date:
30-Mar-01     Release date:   04-May-01    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P62663  (RS3_THET2) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
No UniProt id for this chain
Struc: 83 a.a.
Protein chain
No UniProt id for this chain
Struc: 104 a.a.
Protein chain
No UniProt id for this chain
Struc: 73 a.a.
Protein chain
Pfam   ArchSchema ?
P80381  (RS19_THETH) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
80 a.a.
Protein chain
No UniProt id for this chain
Struc: 99 a.a.
Protein chain
Pfam  
P32193  (RSHX_THETH) - 
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
    reference    
 
 
DOI no: 10.1126/science.1060089 Science 292:883-896 (2001)
PubMed id: 11283358  
 
 
Crystal structure of the ribosome at 5.5 A resolution.
M.M.Yusupov, G.Z.Yusupova, A.Baucom, K.Lieberman, T.N.Earnest, J.H.Cate, H.F.Noller.
 
  ABSTRACT  
 
We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Electron density of tRNA^Met[f] bound to the P site of the 70S ribosome, at 5.5 Å resolution.
Figure 8.
Fig. 8. (A) Interaction of E-tRNA with the ribosome. (B) Secondary structures of 16S and 23S rRNA, showing molecular contacts with A-tRNA (gold), P-tRNA (orange), and E-tRNA (red).
 
  The above figures are reprinted by permission from the AAAs: Science (2001, 292, 883-896) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23262488 M.E.Filbin, B.S.Vollmar, D.Shi, T.Gonen, and J.S.Kieft (2013).
HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.
  Nat Struct Mol Biol, 20, 150-158.  
22525755 M.Selmer, Y.G.Gao, A.Weixlbaumer, and V.Ramakrishnan (2012).
Ribosome engineering to promote new crystal forms.
  Acta Crystallogr D Biol Crystallogr, 68, 578-583.  
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21256733 A.Petrov, G.Kornberg, S.O'Leary, A.Tsai, S.Uemura, and J.D.Puglisi (2011).
Dynamics of the translational machinery.
  Curr Opin Struct Biol, 21, 137-145.  
21133351 B.Liu, J.M.Diamond, D.H.Mathews, and D.H.Turner (2011).
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.
  Biochemistry, 50, 640-653.  
21265782 C.Bricio, L.Alvarez, M.J.Gómez, and J.Berenguer (2011).
Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts.
  Biochem Soc Trans, 39, 249-253.  
21082171 D.Caetano-Anollés, K.M.Kim, J.E.Mittenthal, and G.Caetano-Anollés (2011).
Proteome evolution and the metabolic origins of translation and cellular life.
  J Mol Evol, 72, 14-33.  
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
21370971 D.V.Fedyukina, and S.Cavagnero (2011).
Protein folding at the exit tunnel.
  Annu Rev Biophys, 40, 337-359.  
21419622 F.A.Rey, and W.I.Sundquist (2011).
Macromolecular assemblages.
  Curr Opin Struct Biol, 21, 221-222.  
21857664 J.Fei, A.C.Richard, J.E.Bronson, and R.L.Gonzalez (2011).
Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis.
  Nat Struct Mol Biol, 18, 1043-1051.  
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
  Biochimie, 93, 834-844.  
21530341 N.M.Kumbhar, and K.D.Sonawane (2011).
Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37(th) position in anticodon loop of tRNA(Phe).
  J Mol Graph Model, 29, 935-946.  
21036868 P.W.Rose, B.Beran, C.Bi, W.F.Bluhm, D.Dimitropoulos, D.S.Goodsell, A.Prlic, M.Quesada, G.B.Quinn, J.D.Westbrook, J.Young, B.Yukich, C.Zardecki, H.M.Berman, and P.E.Bourne (2011).
The RCSB Protein Data Bank: redesigned web site and web services.
  Nucleic Acids Res, 39, D392-D401.  
21138965 Q.Sun, A.Vila-Sanjurjo, and M.O'Connor (2011).
Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit-subunit interactions on the 70S ribosome.
  Nucleic Acids Res, 39, 3321-3330.  
21400046 Q.Xie, J.Lin, Y.Qin, J.Zhou, and W.Bu (2011).
Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.
  Protein Cell, 2, 161-170.  
21253643 Q.Zhao, C.Huang, and F.Li (2011).
Phosphorescent heavy-metal complexes for bioimaging.
  Chem Soc Rev, 40, 2508-2524.  
21219455 R.E.Schaub, and C.S.Hayes (2011).
Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7.
  Mol Microbiol, 79, 331-341.  
20798174 S.Kapoor, G.Das, and U.Varshney (2011).
Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA(fMet) selection on the ribosomal P-site in Escherichia coli.
  Nucleic Acids Res, 39, 202-212.  
20034956 A.A.Malygin, and G.G.Karpova (2010).
Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively.
  Nucleic Acids Res, 38, 2089-2098.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
20375101 A.Chirkova, M.D.Erlacher, N.Clementi, M.Zywicki, M.Aigner, and N.Polacek (2010).
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 38, 4844-4855.  
20110260 A.E.Scheunemann, W.D.Graham, F.A.Vendeix, and P.F.Agris (2010).
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.
  Nucleic Acids Res, 38, 3094-3105.  
19691449 A.Fatehullah, C.Doherty, G.Pivato, G.Allen, L.Devine, J.Nelson, and D.J.Timson (2010).
Interactions of the 67 kDa laminin receptor and its precursor with laminin.
  Biosci Rep, 30, 73-79.  
21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
20660012 A.Meskauskas, and J.D.Dinman (2010).
A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site.
  Nucleic Acids Res, 38, 7800-7813.  
19937661 A.Ohman, T.Oman, and M.Oliveberg (2010).
Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55).
  Protein Sci, 19, 183-189.
PDB codes: 2kjv 2kjw
20192783 C.E.Aitken, A.Petrov, and J.D.Puglisi (2010).
Single ribosome dynamics and the mechanism of translation.
  Annu Rev Biophys, 39, 491-513.  
20439768 C.Eichmann, S.Preissler, R.Riek, and E.Deuerling (2010).
Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.
  Proc Natl Acad Sci U S A, 107, 9111-9116.  
20652591 E.Byers, J.Rueger, and L.Bonen (2010).
Impact of genomic environment on mitochondrial rps7 mRNA features in grasses.
  Mol Genet Genomics, 284, 207-216.  
20550657 E.Capriotti, and M.A.Marti-Renom (2010).
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.
  BMC Bioinformatics, 11, 322.  
20095651 E.Posokhova, V.Uversky, and K.A.Martemyanov (2010).
Proteomic identification of Hsc70 as a mediator of RGS9-2 degradation by in vivo interactome analysis.
  J Proteome Res, 9, 1510-1521.  
20334683 F.J.Sun, and G.Caetano-Anollés (2010).
The ancient history of the structure of ribonuclease P and the early origins of Archaea.
  BMC Bioinformatics, 11, 153.  
20552334 F.J.Sun, and G.Caetano-Anollés (2010).
The origin of modern 5S rRNA: a case of relating models of structural history to phylogenetic data.
  J Mol Evol, 71, 3-5.  
20377916 H.S.Bernhardt, and W.P.Tate (2010).
The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?
  Biol Direct, 5, 16.  
20507916 I.Besseová, K.Réblová, N.B.Leontis, and J.Sponer (2010).
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
  Nucleic Acids Res, 38, 6247-6264.  
20963776 J.Berger, and M.Oberhuber (2010).
Chemistry on nucleic acid templates.
  Chem Biodivers, 7, 2581-2615.  
19897649 J.Crandall, M.Rodriguez-Lopez, M.Pfeiffer, B.Mortensen, and A.Buskirk (2010).
rRNA mutations that inhibit transfer-messenger RNA activity on stalled ribosomes.
  J Bacteriol, 192, 553-559.  
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
  21072331 J.Frank (2010).
The Ribosome Comes Alive.
  Isr J Chem, 50, 95-98.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20980660 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB code: 3izd
20584915 J.Sengupta, C.Bussiere, J.Pallesen, M.West, A.W.Johnson, and J.Frank (2010).
Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit.
  J Cell Biol, 189, 1079-1086.  
19952067 K.Réblová, F.Rázga, W.Li, H.Gao, J.Frank, and J.Sponer (2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
  Nucleic Acids Res, 38, 1325-1340.  
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
19946275 M.B.Feldman, D.S.Terry, R.B.Altman, and S.C.Blanchard (2010).
Aminoglycoside activity observed on single pre-translocation ribosome complexes.
  Nat Chem Biol, 6, 54-62.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
20135118 M.Hatamoto, A.Ohashi, and H.Imachi (2010).
Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology.
  Appl Microbiol Biotechnol, 86, 397-402.  
19965869 M.R.Sharma, A.Dönhöfer, C.Barat, V.Marquez, P.P.Datta, P.Fucini, D.N.Wilson, and R.K.Agrawal (2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
  J Biol Chem, 285, 4006-4014.  
20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
  J Struct Biol, 170, 164-171.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
20631791 N.Fischer, A.L.Konevega, W.Wintermeyer, M.V.Rodnina, and H.Stark (2010).
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
  Nature, 466, 329-333.  
20427512 P.C.Whitford, P.Geggier, R.B.Altman, S.C.Blanchard, J.N.Onuchic, and K.Y.Sanbonmatsu (2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
  RNA, 16, 1196-1204.  
20358253 R.Sabate, N.S.de Groot, and S.Ventura (2010).
Protein folding and aggregation in bacteria.
  Cell Mol Life Sci, 67, 2695-2715.  
20419210 S.De, K.Mahata, and M.Schmittel (2010).
Metal-coordination-driven dynamic heteroleptic architectures.
  Chem Soc Rev, 39, 1555-1575.  
19965768 S.Kimura, and T.Suzuki (2010).
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
  Nucleic Acids Res, 38, 1341-1352.  
20208546 S.L.He, and R.Green (2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
  Nat Struct Mol Biol, 17, 465-470.  
19969550 T.Lumsden, A.A.Bentley, W.Beutler, A.Ghosh, O.Galkin, and A.A.Komar (2010).
Yeast strains with N-terminally truncated ribosomal protein S5: implications for the evolution, structure and function of the Rps5/Rps7 proteins.
  Nucleic Acids Res, 38, 1261-1272.  
21110883 W.Ma (2010).
The scenario on the origin of translation in the RNA world: in principle of replication parsimony.
  Biol Direct, 5, 65.  
21054500 W.S.Song, S.M.Ryou, H.M.Kim, C.O.Jeon, J.M.Kim, S.H.Han, S.W.Kim, J.P.Szatkiewicz, P.R.Cunningham, and K.Lee (2010).
Functional investigation of residue G791 of Escherichia coli 16S rRNA: implication of initiation factor 1 in the restoration of P-site function.
  FEMS Microbiol Lett, 313, 141-147.  
19854950 Y.Lustig, C.Wachtel, M.Safro, L.Liu, and S.Michaeli (2010).
'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target.
  Nucleic Acids Res, 38, e5.  
19820108 A.Baudin-Baillieu, C.Fabret, X.H.Liang, D.Piekna-Przybylska, M.J.Fournier, and J.P.Rousset (2009).
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy.
  Nucleic Acids Res, 37, 7665-7677.  
19424134 A.Bhattacharya (2009).
Protein structures: Structures of desire.
  Nature, 459, 24-27.  
19095617 A.Devaraj, S.Shoji, E.D.Holbrook, and K.Fredrick (2009).
A role for the 30S subunit E site in maintenance of the translational reading frame.
  RNA, 15, 255-265.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
  Structure, 17, 1605-1613.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19553343 B.Llano-Sotelo, R.P.Hickerson, L.Lancaster, H.F.Noller, and A.S.Mankin (2009).
Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.
  RNA, 15, 1597-1604.  
19279186 C.Hsiao, and L.D.Williams (2009).
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 37, 3134-3142.  
19445952 C.Laing, and T.Schlick (2009).
Analysis of four-way junctions in RNA structures.
  J Mol Biol, 390, 547-559.  
19746388 C.Switzer (2009).
A missing prebiotic link: discovery of a plausible synthesis of pyrimidine nucleotides.
  Chembiochem, 10, 2591-2593.  
20004159 C.W.Carter (2009).
E pluribus tres: the 2009 nobel prize in chemistry.
  Structure, 17, 1558-1561.  
19036786 D.Benelli, S.Marzi, C.Mancone, T.Alonzi, A.la Teana, and P.Londei (2009).
Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya.
  Nucleic Acids Res, 37, 256-267.  
19861425 D.Hasenöhrl, A.Fabbretti, P.Londei, C.O.Gualerzi, and U.Bläsi (2009).
Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus.
  RNA, 15, 2288-2298.  
19952110 D.M.Landry, M.I.Hertz, and S.R.Thompson (2009).
RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs.
  Genes Dev, 23, 2753-2764.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19118261 D.Pan, H.Qin, and B.S.Cooperman (2009).
Synthesis and functional activity of tRNAs labeled with fluorescent hydrazides in the D-loop.
  RNA, 15, 346-354.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19156357 F.Cava, A.Hidalgo, and J.Berenguer (2009).
Thermus thermophilus as biological model.
  Extremophiles, 13, 213-231.  
19639237 F.J.Sun, and G.Caetano-Anollés (2009).
The evolutionary history of the structure of 5S ribosomal RNA.
  J Mol Evol, 69, 430-443.  
19696344 G.Blaha, R.E.Stanley, and T.A.Steitz (2009).
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
  Science, 325, 966-970.
PDB codes: 3huw 3hux 3huy 3huz
19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
  J Proteome Res, 8, 3390-3402.  
19897894 H.J.Ha, W.S.Song, H.M.Kim, H.S.Son, and K.Lee (2009).
Functional study of the residue C899 in the 900 tetraloop of Escherichia coli small subunit ribosomal RNA.
  Biosci Biotechnol Biochem, 73, 2544-2546.  
19168615 H.M.Kim, S.M.Ryou, W.S.Song, S.H.Sim, C.J.Cha, S.H.Han, N.C.Ha, J.H.Kim, J.Bae, P.R.Cunningham, and K.Lee (2009).
Genetic analysis of the invariant residue G791 in Escherichia coli 16S rRNA implicates RelA in ribosome function.
  J Bacteriol, 191, 2042-2050.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19571367 I.Tinoco, and J.D.Wen (2009).
Simulation and analysis of single-ribosome translation.
  Phys Biol, 6, 25006.  
19647434 J.B.Munro, K.Y.Sanbonmatsu, C.M.Spahn, and S.C.Blanchard (2009).
Navigating the ribosome's metastable energy landscape.
  Trends Biochem Sci, 34, 390-400.  
19840948 J.Batisse, C.Batisse, A.Budd, B.Böttcher, and E.Hurt (2009).
Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure.
  J Biol Chem, 284, 34911-34917.  
19229291 J.C.Schuette, F.V.Murphy, A.C.Kelley, J.R.Weir, J.Giesebrecht, S.R.Connell, J.Loerke, T.Mielke, W.Zhang, P.A.Penczek, V.Ramakrishnan, and C.M.Spahn (2009).
GTPase activation of elongation factor EF-Tu by the ribosome during decoding.
  EMBO J, 28, 755-765.
PDB codes: 3fic 3fin
19258537 J.F.Atkins, and G.R.Björk (2009).
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment.
  Microbiol Mol Biol Rev, 73, 178-210.  
19717422 J.Fei, J.E.Bronson, J.M.Hofman, R.L.Srinivas, C.H.Wiggins, and R.L.Gonzalez (2009).
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.
  Proc Natl Acad Sci U S A, 106, 15702-15707.  
19702336 J.L.Miller, H.Cimen, H.Koc, and E.C.Koc (2009).
Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
  J Proteome Res, 8, 4789-4798.  
20005796 J.R.Williamson, V.Ramakrishnan, T.Steitz, and A.Yonath (2009).
The ribosome at atomic resolution.
  Cell, 139, 1041-1043.  
19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.
  Nature, 457, 977-980.  
19285158 K.L.Fung, and M.M.Gottesman (2009).
A synonymous polymorphism in a common MDR1 (ABCB1) haplotype shapes protein function.
  Biochim Biophys Acta, 1794, 860-871.  
19082014 K.Rijal, and C.S.Chow (2009).
A new role for cisplatin: probing ribosomal RNA structure.
  Chem Commun (Camb), (), 107-109.  
19734347 L.M.Sharpe Elles, M.T.Sykes, J.R.Williamson, and O.C.Uhlenbeck (2009).
A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit.
  Nucleic Acids Res, 37, 6503-6514.  
19144906 M.A.Jonikas, R.J.Radmer, A.Laederach, R.Das, S.Pearlman, D.Herschlag, and R.B.Altman (2009).
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.
  RNA, 15, 189-199.  
19812110 M.A.Jonikas, R.J.Radmer, and R.B.Altman (2009).
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
  Bioinformatics, 25, 3259-3266.  
19767615 M.Messmer, J.Pütz, T.Suzuki, T.Suzuki, C.Sauter, M.Sissler, and F.Catherine (2009).
Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.
  Nucleic Acids Res, 37, 6881-6895.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
19497863 M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, and R.K.Agrawal (2009).
Structure of a mitochondrial ribosome with minimal RNA.
  Proc Natl Acad Sci U S A, 106, 9637-9642.
PDB codes: 3iy8 3iy9
19903202 M.Sakamoto, S.Noguchi, S.Kawashima, Y.Okada, T.Enomoto, M.Seki, and M.Horikoshi (2009).
Global analysis of mutual interaction surfaces of nucleosomes with comprehensive point mutants.
  Genes Cells, 14, 1271-1330.  
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
19628400 N.D.Abeydeera, and C.S.Chow (2009).
Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA.
  Bioorg Med Chem, 17, 5887-5893.  
19004020 O.Kurkcuoglu, Z.Kurkcuoglu, P.Doruker, and R.L.Jernigan (2009).
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling.
  Proteins, 75, 837-845.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19190181 P.V.Cornish, D.N.Ermolenko, D.W.Staple, L.Hoang, R.P.Hickerson, H.F.Noller, and T.Ha (2009).
Following movement of the L1 stalk between three functional states in single ribosomes.
  Proc Natl Acad Sci U S A, 106, 2571-2576.  
19595714 R.A.Marshall, C.E.Aitken, and J.D.Puglisi (2009).
GTP hydrolysis by IF2 guides progression of the ribosome into elongation.
  Mol Cell, 35, 37-47.  
19723687 R.R.Stocsits, H.Letsch, J.Hertel, B.Misof, and P.F.Stadler (2009).
Accurate and efficient reconstruction of deep phylogenies from structured RNAs.
  Nucleic Acids Res, 37, 6184-6193.  
19329641 R.Yang, L.R.Cruz-Vera, and C.Yanofsky (2009).
23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction.
  J Bacteriol, 191, 3445-3450.  
19082769 S.Dutta, K.Burkhardt, J.Young, G.J.Swaminathan, T.Matsuura, K.Henrick, H.Nakamura, and H.M.Berman (2009).
Data deposition and annotation at the worldwide protein data bank.
  Mol Biotechnol, 42, 1.  
19305403 S.Ledoux, M.Olejniczak, and O.C.Uhlenbeck (2009).
A sequence element that tunes Escherichia coli tRNA(Ala)(GGC) to ensure accurate decoding.
  Nat Struct Mol Biol, 16, 359-364.  
19627982 S.P.Chan, and F.J.Slack (2009).
Ribosomal protein RPS-14 modulates let-7 microRNA function in Caenorhabditis elegans.
  Dev Biol, 334, 152-160.  
19432457 S.P.Edmondson, J.Turri, K.Smith, A.Clark, and J.W.Shriver (2009).
Structure, stability, and flexibility of ribosomal protein L14e from Sulfolobus solfataricus.
  Biochemistry, 48, 5553-5562.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19203377 T.Ivry, S.Michal, A.Avihoo, G.Sapiro, and D.Barash (2009).
An image processing approach to computing distances between RNA secondary structures dot plots.
  Algorithms Mol Biol, 4, 4.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19486296 T.Tenson, and V.Hauryliuk (2009).
Does the ribosome have initiation and elongation modes of translation?
  Mol Microbiol, 72, 1310-1315.  
19643000 W.Huggins, S.K.Ghosh, and P.Wollenzien (2009).
Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.
  BMC Struct Biol, 9, 49.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
19628622 X.H.Liang, Q.Liu, and M.J.Fournier (2009).
Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing.
  RNA, 15, 1716-1728.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
19561193 Y.Yu, A.Marintchev, V.G.Kolupaeva, A.Unbehaun, T.Veryasova, S.C.Lai, P.Hong, G.Wagner, C.U.Hellen, and T.V.Pestova (2009).
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
  Nucleic Acids Res, 37, 5167-5182.  
18177894 A.A.Saraiya, T.N.Lamichhane, C.S.Chow, J.SantaLucia, and P.R.Cunningham (2008).
Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.
  J Mol Biol, 376, 645-657.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18263608 A.Meskauskas, J.R.Russ, and J.D.Dinman (2008).
Structure/function analysis of yeast ribosomal protein L2.
  Nucleic Acids Res, 36, 1826-1835.  
18218711 B.Wu, A.Yee, Y.J.Huang, T.A.Ramelot, J.R.Cort, A.Semesi, J.W.Jung, W.Lee, G.T.Montelione, M.A.Kennedy, and C.H.Arrowsmith (2008).
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain.
  Protein Sci, 17, 583-588.
PDB code: 1rq6
18755841 C.M.Zhang, C.Liu, T.Christian, H.Gamper, J.Rozenski, D.Pan, J.B.Randolph, E.Wickstrom, B.S.Cooperman, and Y.M.Hou (2008).
Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.
  RNA, 14, 2245-2253.  
18683165 C.Voisset, J.Y.Thuret, D.Tribouillard-Tanvier, S.J.Saupe, and M.Blondel (2008).
Tools for the study of ribosome-borne protein folding activity.
  Biotechnol J, 3, 1033-1040.  
17981968 C.Wicker-Planquart, A.E.Foucher, M.Louwagie, R.A.Britton, and J.M.Jault (2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
  J Bacteriol, 190, 681-690.  
18448426 D.Pan, C.M.Zhang, S.Kirillov, Y.M.Hou, and B.S.Cooperman (2008).
Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle.
  J Biol Chem, 283, 18431-18440.  
17947322 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2008).
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.
  Nucleic Acids Res, 36, D178-D183.  
18755835 E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
  RNA, 14, 2234-2244.  
18190515 F.Cava, M.A.de Pedro, E.Blas-Galindo, G.S.Waldo, L.F.Westblade, and J.Berenguer (2008).
Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology.
  Environ Microbiol, 10, 605-613.  
18369418 F.J.Sun, and G.Caetano-Anollés (2008).
Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.
  PLoS Comput Biol, 4, e1000018.  
18058157 F.J.Sun, and G.Caetano-Anollés (2008).
The Origin and Evolution of tRNA Inferred from Phylogenetic Analysis of Structure.
  J Mol Evol, 66, 21-35.  
18288206 G.Das, D.K.Thotala, S.Kapoor, S.Karunanithi, S.S.Thakur, N.S.Singh, and U.Varshney (2008).
Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli.
  EMBO J, 27, 840-851.  
18201202 H.Aoki, J.Xu, A.Emili, J.G.Chosay, A.Golshani, and M.C.Ganoza (2008).
Interactions of elongation factor EF-P with the Escherichia coli ribosome.
  FEBS J, 275, 671-681.  
18625614 H.David-Eden, and Y.Mandel-Gutfreund (2008).
Revealing unique properties of the ribosome using a network based analysis.
  Nucleic Acids Res, 36, 4641-4652.  
18003936 H.Fan-Minogue, and D.M.Bedwell (2008).
Eukaryotic ribosomal RNA determinants of aminoglycoside resistance and their role in translational fidelity.
  RNA, 14, 148-157.  
18844986 H.Grosjean, C.Gaspin, C.Marck, W.A.Decatur, and V.de Crécy-Lagard (2008).
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
  BMC Genomics, 9, 470.  
18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
  Biophys J, 95, 5962-5973.  
18523488 I.J.Chen, I.A.Wang, L.R.Tai, and A.Lin (2008).
The role of expansion segment of human ribosomal protein L35 in nuclear entry, translation activity, and endoplasmic reticulum docking.
  Biochem Cell Biol, 86, 271-277.  
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
  Biopolymers, 89, 565-577.  
18394159 J.C.Zweers, I.Barák, D.Becher, A.J.Driessen, M.Hecker, V.P.Kontinen, M.J.Saller, L.Vavrová, and J.M.van Dijl (2008).
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes.
  Microb Cell Fact, 7, 10.  
18327250 J.D.Wen, L.Lancaster, C.Hodges, A.C.Zeri, S.H.Yoshimura, H.F.Noller, C.Bustamante, and I.Tinoco (2008).
Following translation by single ribosomes one codon at a time.
  Nature, 452, 598-603.  
18471980 J.Fei, P.Kosuri, D.D.MacDougall, and R.L.Gonzalez (2008).
Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.
  Mol Cell, 30, 348-359.  
18221266 J.H.Yoo, and U.L.RajBhandary (2008).
Requirements for translation re-initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3.
  Mol Microbiol, 67, 1012-1026.  
18931791 J.P.Desaulniers, Y.C.Chang, R.Aduri, S.C.Abeysirigunawardena, J.SantaLucia, and C.S.Chow (2008).
Pseudouridines in rRNA helix 69 play a role in loop stacking interactions.
  Org Biomol Chem, 6, 3892-3895.  
20107615 J.P.Schmidt, S.L.Delp, M.A.Sherman, C.A.Taylor, V.S.Pande, and R.B.Altman (2008).
The Simbios National Center: Systems Biology in Motion.
  Proc IEEE Inst Electr Electron Eng, 96, 1266-1280.  
18515544 J.S.Pfingsten, and J.S.Kieft (2008).
RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.
  RNA, 14, 1255-1263.  
18644383 J.Sengupta, J.Nilsson, R.Gursky, M.Kjeldgaard, P.Nissen, and J.Frank (2008).
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
  J Mol Biol, 382, 179-187.
PDB codes: 3dny 3dwu
18637734 K.Bakowska-Zywicka, A.M.Kietrys, and T.Twardowski (2008).
Antisense oligonucleotides targeting universally conserved 26S rRNA domains of plant ribosomes at different steps of polypeptide elongation.
  Oligonucleotides, 18, 175-186.  
18439255 K.Katoh, and H.Toh (2008).
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
  BMC Bioinformatics, 9, 212.  
18820021 K.Krishnan, and A.M.Flower (2008).
Suppression of DeltabipA phenotypes in Escherichia coli by abolishment of pseudouridylation at specific sites on the 23S rRNA.
  J Bacteriol, 190, 7675-7683.  
18365744 K.N.Bulygin, S.Baouz-Drahy, A.Favre, A.G.Ven'iaminova, D.M.Graíífer, and G.G.Karpova (2008).
[The environment of tRNA 3'-terminus in 80S ribosome A and P sites].
  Bioorg Khim, 34, 96.  
18485067 L.E.Lancaster, A.Savelsbergh, C.Kleanthous, W.Wintermeyer, and M.V.Rodnina (2008).
Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes.
  Mol Microbiol, 69, 390-401.  
18951096 L.Garcia-Ortega, J.Stephen, and S.Joseph (2008).
Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation.
  Mol Cell, 32, 292-299.  
18755834 L.Lancaster, N.J.Lambert, E.J.Maklan, L.H.Horan, and H.F.Noller (2008).
The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.
  RNA, 14, 1999-2012.  
18567815 M.A.Borovinskaya, S.Shoji, K.Fredrick, and J.H.Cate (2008).
Structural basis for hygromycin B inhibition of protein biosynthesis.
  RNA, 14, 1590-1599.
PDB codes: 3df1 3df2 3df3 3df4
18369182 M.Beringer (2008).
Modulating the activity of the peptidyl transferase center of the ribosome.
  RNA, 14, 795-801.  
18596689 M.Laurberg, H.Asahara, A.Korostelev, J.Zhu, S.Trakhanov, and H.F.Noller (2008).
Structural basis for translation termination on the 70S ribosome.
  Nature, 454, 852-857.
PDB codes: 3d5a 3d5b 3d5c 3d5d
18187576 M.Simonović, and T.A.Steitz (2008).
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.
  Proc Natl Acad Sci U S A, 105, 500-505.  
19029596 O.Kurkcuoglu, P.Doruker, T.Z.Sen, A.Kloczkowski, and R.L.Jernigan (2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
  Phys Biol, 5, 46005.  
18653533 P.Barraud, E.Schmitt, Y.Mechulam, F.Dardel, and C.Tisné (2008).
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
  Nucleic Acids Res, 36, 4894-4901.
PDB codes: 3cw5 3cw6
17937599 P.C.Bevilacqua, and J.M.Blose (2008).
Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.
  Annu Rev Phys Chem, 59, 79.  
18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure, 16, 535-548.
PDB codes: 2zkq 2zkr
18344525 P.Y.Liao, P.Gupta, A.N.Petrov, J.D.Dinman, and K.H.Lee (2008).
A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting.
  Nucleic Acids Res, 36, 2619-2629.  
18203922 Q.Vicens, M.A.Allen, S.D.Gilbert, B.Reznik, A.R.Gooding, R.T.Batey, and T.R.Cech (2008).
The Cech Symposium: a celebration of 25 years of ribozymes, 10 years of TERT, and 60 years of Tom.
  RNA, 14, 397-403.  
18518820 R.A.Marshall, C.E.Aitken, M.Dorywalska, and J.D.Puglisi (2008).
Translation at the single-molecule level.
  Annu Rev Biochem, 77, 177-203.  
18824686 R.A.Marshall, M.Dorywalska, and J.D.Puglisi (2008).
Irreversible chemical steps control intersubunit dynamics during translation.
  Proc Natl Acad Sci U S A, 105, 15364-15369.  
18234219 R.D.Pai, W.Zhang, B.S.Schuwirth, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2008).
Structural Insights into ribosome recycling factor interactions with the 70S ribosome.
  J Mol Biol, 376, 1334-1347.  
18755836 R.Ero, L.Peil, A.Liiv, and J.Remme (2008).
Identification of pseudouridine methyltransferase in Escherichia coli.
  RNA, 14, 2223-2233.  
18362332 R.N.Evans, G.Blaha, S.Bailey, and T.A.Steitz (2008).
The structure of LepA, the ribosomal back translocase.
  Proc Natl Acad Sci U S A, 105, 4673-4678.
PDB code: 3cb4
18606739 R.Raghavan, L.D.Hicks, and M.F.Minnick (2008).
Toxic introns and parasitic intein in Coxiella burnetii: legacies of a promiscuous past.
  J Bacteriol, 190, 5934-5943.  
18203742 R.Rakauskaite, and J.D.Dinman (2008).
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
  Nucleic Acids Res, 36, 1497-1507.  
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
18268024 S.C.Abeysirigunawardena, and C.S.Chow (2008).
pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA.
  RNA, 14, 782-792.  
18221556 S.L.Liu, and K.Adams (2008).
Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids.
  BMC Evol Biol, 8, 25.  
18304947 S.Muller, F.Leclerc, I.Behm-Ansmant, J.B.Fourmann, B.Charpentier, and C.Branlant (2008).
Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
  Nucleic Acids Res, 36, 2459-2475.  
19172743 S.R.Connell, M.Topf, Y.Qin, D.N.Wilson, T.Mielke, P.Fucini, K.H.Nierhaus, and C.M.Spahn (2008).
A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation.
  Nat Struct Mol Biol, 15, 910-915.
PDB code: 3deg
18338356 S.Takahashi, R.Akita, H.Matsuno, H.Furusawa, Y.Shimizu, T.Ueda, and Y.Okahata (2008).
70 S ribosomes bind to Shine-Dalgarno sequences without required dissociations.
  Chembiochem, 9, 870-873.  
18853276 T.A.Isenbarger, C.E.Carr, S.S.Johnson, M.Finney, G.M.Church, W.Gilbert, M.T.Zuber, and G.Ruvkun (2008).
The most conserved genome segments for life detection on Earth and other planets.
  Orig Life Evol Biosph, 38, 517-533.  
18382121 T.A.Steitz (2008).
Structural insights into the functions of the large ribosomal subunit, a major antibiotic target.
  Keio J Med, 57, 1.  
18430223 T.F.Smith, J.C.Lee, R.R.Gutell, and H.Hartman (2008).
The origin and evolution of the ribosome.
  Biol Direct, 3, 16.  
18399722 T.Herman, S.Colton, and M.Franzen (2008).
Rethinking outreach: teaching the process of science through modeling.
  PLoS Biol, 6, e86.  
18805973 T.Monshupanee, S.T.Gregory, S.Douthwaite, W.Chungjatupornchai, and A.E.Dahlberg (2008).
Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.
  J Bacteriol, 190, 7754-7761.  
18548002 T.Saito, D.M.Owen, F.Jiang, J.Marcotrigiano, and M.Gale (2008).
Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA.
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18456707 T.Yokoyama, and T.Suzuki (2008).
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
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19020518 W.Li, X.Agirrezabala, J.Lei, L.Bouakaz, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, S.Sanyal, M.Ehrenberg, and J.Frank (2008).
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
  EMBO J, 27, 3322-3331.
PDB codes: 3ep2 3eq3 3eq4
18951087 X.Agirrezabala, J.Lei, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, and J.Frank (2008).
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
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17401565 X.Wang, G.Kapral, L.Murray, D.Richardson, J.Richardson, and J.Snoeyink (2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
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17105995 A.Barkan, L.Klipcan, O.Ostersetzer, T.Kawamura, Y.Asakura, and K.P.Watkins (2007).
The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.
  RNA, 13, 55-64.  
17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
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17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
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17369838 A.L.Konevega, N.Fischer, Y.P.Semenkov, H.Stark, W.Wintermeyer, and M.V.Rodnina (2007).
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
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17683199 A.L.Manuell, J.Quispe, and S.P.Mayfield (2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
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17379815 A.V.Manuilov, S.S.Hixson, and R.A.Zimmermann (2007).
New photoreactive tRNA derivatives for probing the peptidyl transferase center of the ribosome.
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17660830 A.Weixlbaumer, S.Petry, C.M.Dunham, M.Selmer, A.C.Kelley, and V.Ramakrishnan (2007).
Crystal structure of the ribosome recycling factor bound to the ribosome.
  Nat Struct Mol Biol, 14, 733-737.
PDB codes: 2v46 2v47 2v48 2v49
17532253 B.Felden (2007).
RNA structure: experimental analysis.
  Curr Opin Microbiol, 10, 286-291.  
17643374 C.Barat, P.P.Datta, V.S.Raj, M.R.Sharma, H.Kaji, A.Kaji, and R.K.Agrawal (2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
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17287347 C.Hyeon, and J.N.Onuchic (2007).
Internal strain regulates the nucleotide binding site of the kinesin leading head.
  Proc Natl Acad Sci U S A, 104, 2175-2180.  
17621298 C.Köhrer, and U.L.RajBhandary (2007).
An evolved ribosome for genetic code expansion.
  Nat Biotechnol, 25, 745-746.  
17660276 C.L.Sanders, and J.F.Curran (2007).
Genetic analysis of the E site during RF2 programmed frameshifting.
  RNA, 13, 1483-1491.  
17416634 C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, and V.Ramakrishnan (2007).
Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.
  RNA, 13, 817-823.
PDB codes: 2uxb 2uxc 2uxd
  17894445 C.S.Chow, T.N.Lamichhane, and S.K.Mahto (2007).
Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications.
  ACS Chem Biol, 2, 610-619.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
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17914224 D.Bhattacharyya, S.C.Koripella, A.Mitra, V.B.Rajendran, and B.Sinha (2007).
Theoretical analysis of noncanonical base pairing interactions in RNA molecules.
  J Biosci, 32, 809-825.  
17446867 D.J.Taylor, J.Nilsson, A.R.Merrill, G.R.Andersen, P.Nissen, and J.Frank (2007).
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.
  EMBO J, 26, 2421-2431.
PDB codes: 2p8w 2p8x 2p8y 2p8z
17515906 D.N.Ermolenko, P.C.Spiegel, Z.K.Majumdar, R.P.Hickerson, R.M.Clegg, and H.F.Noller (2007).
The antibiotic viomycin traps the ribosome in an intermediate state of translocation.
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17317625 D.Pan, S.V.Kirillov, and B.S.Cooperman (2007).
Kinetically competent intermediates in the translocation step of protein synthesis.
  Mol Cell, 25, 519-529.  
17283215 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2007).
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
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17189261 D.V.Lesnyak, J.Osipiuk, T.Skarina, P.V.Sergiev, A.A.Bogdanov, A.Edwards, A.Savchenko, A.Joachimiak, and O.A.Dontsova (2007).
Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure.
  J Biol Chem, 282, 5880-5887.
PDB code: 2fpo
17652323 E.C.Kouvela, G.V.Gerbanas, M.A.Xaplanteri, A.D.Petropoulos, G.P.Dinos, and D.L.Kalpaxis (2007).
Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine.
  Nucleic Acids Res, 35, 5108-5119.  
17621307 E.S.Poole, D.J.Young, M.E.Askarian-Amiri, D.J.Scarlett, and W.P.Tate (2007).
Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome.
  Cell Res, 17, 591-607.  
17651434 E.V.Ivanova, P.M.Kolosov, B.Birdsall, G.Kelly, A.Pastore, L.L.Kisselev, and V.I.Polshakov (2007).
Eukaryotic class 1 translation termination factor eRF1--the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis.
  FEBS J, 274, 4223-4237.
PDB code: 2hst
17553840 F.Rázga, J.Koca, A.Mokdad, and J.Sponer (2007).
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
  Nucleic Acids Res, 35, 4007-4017.  
17478509 G.Emmerechts, S.Barbé, P.Herdewijn, J.Anné, and J.Rozenski (2007).
Post-transcriptional modification mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays.
  Nucleic Acids Res, 35, 3494-3503.  
17088492 G.Hirokawa, H.Kaji, and A.Kaji (2007).
Inhibition of antiassociation activity of translation initiation factor 3 by paromomycin.
  Antimicrob Agents Chemother, 51, 175-180.  
17872509 G.N.Basturea, and M.P.Deutscher (2007).
Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE.
  RNA, 13, 1969-1976.  
17688253 G.Todd, and K.Karbstein (2007).
RNA takes center stage.
  Biopolymers, 87, 275-278.  
17693476 H.D.Kim, J.D.Puglisi, and S.Chu (2007).
Fluctuations of transfer RNAs between classical and hybrid states.
  Biophys J, 93, 3575-3582.  
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB code: 2jq7
17632571 I.Brierley, S.Pennell, and R.J.Gilbert (2007).
Viral RNA pseudoknots: versatile motifs in gene expression and replication.
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18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
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17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
17245450 J.L.Baxter-Roshek, A.N.Petrov, and J.D.Dinman (2007).
Optimization of ribosome structure and function by rRNA base modification.
  PLoS ONE, 2, e174.  
17434183 J.Nilsson, J.Sengupta, R.Gursky, P.Nissen, and J.Frank (2007).
Comparison of fungal 80 S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments.
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17553838 K.Kitahara, A.Kajiura, N.S.Sato, and T.Suzuki (2007).
Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2.
  Nucleic Acids Res, 35, 4018-4029.  
17452365 K.Lagesen, P.Hallin, E.A.Rødland, H.H.Staerfeldt, T.Rognes, and D.W.Ussery (2007).
RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
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17159993 L.Cochella, J.L.Brunelle, and R.Green (2007).
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.
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17360328 L.H.Horan, and H.F.Noller (2007).
Intersubunit movement is required for ribosomal translocation.
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17721443 L.Jenner, B.Rees, M.Yusupov, and G.Yusupova (2007).
Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography.
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17376481 L.M.Dutcă, I.Jagannathan, J.F.Grondek, and G.M.Culver (2007).
Temperature-dependent RNP conformational rearrangements: analysis of binary complexes of primary binding proteins with 16 S rRNA.
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17711575 L.Pnueli, and Y.Arava (2007).
Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9.
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17660832 M.A.Borovinskaya, R.D.Pai, W.Zhang, B.S.Schuwirth, J.M.Holton, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2007).
Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
  Nat Struct Mol Biol, 14, 727-732.
PDB codes: 2qal 2qam 2qan 2qao 2qb9 2qba 2qbb 2qbc 2qbd 2qbe 2qbf 2qbg 2qbh 2qbi 2qbj 2qbk 2z4k 2z4l 2z4m 2z4n
17570820 M.Beringer, and M.V.Rodnina (2007).
Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs.
  Biol Chem, 388, 687-691.  
17499039 M.Beringer, and M.V.Rodnina (2007).
The ribosomal peptidyl transferase.
  Mol Cell, 26, 311-321.  
17379816 M.E.Saks, and J.S.Conery (2007).
Anticodon-dependent conservation of bacterial tRNA gene sequences.
  RNA, 13, 651-660.  
18032607 M.Ejby, M.A.Sørensen, and S.Pedersen (2007).
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination.
  Proc Natl Acad Sci U S A, 104, 19410-19415.  
17521915 M.J.Suh, S.Pourshahian, and P.A.Limbach (2007).
Developing limited proteolysis and mass spectrometry for the characterization of ribosome topography.
  J Am Soc Mass Spectrom, 18, 1304-1317.  
17804668 M.Kaczanowska, and M.Rydén-Aulin (2007).
Ribosome biogenesis and the translation process in Escherichia coli.
  Microbiol Mol Biol Rev, 71, 477-494.  
17704133 M.Léger, D.Dulude, S.V.Steinberg, and L.Brakier-Gingras (2007).
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
  Nucleic Acids Res, 35, 5581-5592.  
17937767 M.Leppik, L.Peil, K.Kipper, A.Liiv, and J.Remme (2007).
Substrate specificity of the pseudouridine synthase RluD in Escherichia coli.
  FEBS J, 274, 5759-5766.  
  18007048 M.Nishimura, T.Kaminishi, M.Kawazoe, M.Shirouzu, C.Takemoto, S.Yokoyama, A.Tanaka, S.Sugano, T.Yoshida, T.Ohkubo, and Y.Kobayashi (2007).
Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 950-952.  
17828421 M.O'Connor (2007).
Selection for intragenic suppressors of lethal 23S rRNA mutations in Escherichia coli identifies residues important for ribosome assembly and function.
  Mol Genet Genomics, 278, 677-687.  
17564727 M.O'connor (2007).
Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli.
  Mol Genet Genomics, 278, 307-315.  
18042701 M.R.Sharma, D.N.Wilson, P.P.Datta, C.Barat, F.Schluenzen, P.Fucini, and R.K.Agrawal (2007).
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
  Proc Natl Acad Sci U S A, 104, 19315-19320.
PDB codes: 3bbn 3bbo
17157507 M.V.Rodnina, M.Beringer, and W.Wintermeyer (2007).
How ribosomes make peptide bonds.
  Trends Biochem Sci, 32, 20-26.  
17586816 N.Demeshkina, G.Hirokawa, A.Kaji, and H.Kaji (2007).
Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP.
  Nucleic Acids Res, 35, 4597-4607.  
18033580 N.Dixon, L.S.Wong, T.H.Geerlings, and J.Micklefield (2007).
Cellular targets of natural products.
  Nat Prod Rep, 24, 1288-1310.  
17901157 O.Galkin, A.A.Bentley, S.Gupta, B.A.Compton, B.Mazumder, T.G.Kinzy, W.C.Merrick, M.Hatzoglou, T.V.Pestova, C.U.Hellen, and A.A.Komar (2007).
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5.
  RNA, 13, 2116-2128.  
17565764 O.Schiemann, and T.F.Prisner (2007).
Long-range distance determinations in biomacromolecules by EPR spectroscopy.
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17391549 P.C.Bevilacqua, A.L.Cerrone-Szakal, and N.A.Siegfried (2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.
  Q Rev Biophys, 40, 55-85.  
17996707 P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, and R.K.Agrawal (2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.
  Mol Cell, 28, 434-445.
PDB codes: 2dyj 2r1c 2r1g
17872507 P.P.Vaidyanathan, M.P.Deutscher, and A.Malhotra (2007).
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.
  RNA, 13, 1868-1876.  
17389639 P.V.Sergiev, A.A.Bogdanov, and O.A.Dontsova (2007).
Ribosomal RNA guanine-(N2)-methyltransferases and their targets.
  Nucleic Acids Res, 35, 2295-2301.  
17951333 R.L.Gonzalez, S.Chu, and J.D.Puglisi (2007).
Thiostrepton inhibition of tRNA delivery to the ribosome.
  RNA, 13, 2091-2097.  
  16957327 R.L.Jernigan, and A.Kloczkowski (2007).
Packing regularities in biological structures relate to their dynamics.
  Methods Mol Biol, 350, 251-276.  
17660285 R.Leipuviene, and G.R.Björk (2007).
Alterations in the two globular domains or in the connecting alpha-helix of bacterial ribosomal protein L9 induces +1 frameshifts.
  J Bacteriol, 189, 7024-7031.  
17644584 R.Raghavan, S.R.Miller, L.D.Hicks, and M.F.Minnick (2007).
The unusual 23S rRNA gene of Coxiella burnetii: two self-splicing group I introns flank a 34-base-pair exon, and one element lacks the canonical omegaG.
  J Bacteriol, 189, 6572-6579.  
17960736 R.Weerasekera, Y.M.She, K.A.Markham, Y.Bai, N.Opalka, S.Orlicky, F.Sicheri, T.Kislinger, and G.Schmitt-Ulms (2007).
Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes.
  Proteomics, 7, 3835-3852.  
17080418 S.E.McDowell, N.Spacková, J.Sponer, and N.G.Walter (2007).
Molecular dynamics simulations of RNA: an in silico single molecule approach.
  Biopolymers, 85, 169-184.  
17996708 S.Ferreira-Cerca, G.Pöll, H.Kühn, A.Neueder, S.Jakob, H.Tschochner, and P.Milkereit (2007).
Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins.
  Mol Cell, 28, 446-457.  
17517772 S.L.Ameres, D.Shcherbakov, E.Nikonova, W.Piendl, R.Schroeder, and K.Semrad (2007).
RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition.
  Nucleic Acids Res, 35, 3752-3763.  
17889647 S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, and B.P.Klaholz (2007).
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
  Cell, 130, 1019-1031.
PDB code: 2vaz
17349960 S.R.Connell, C.Takemoto, D.N.Wilson, H.Wang, K.Murayama, T.Terada, M.Shirouzu, M.Rost, M.Schüler, J.Giesebrecht, M.Dabrowski, T.Mielke, P.Fucini, S.Yokoyama, and C.M.Spahn (2007).
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
  Mol Cell, 25, 751-764.
PDB code: 2om7
17468501 S.Smit, J.Widmann, and R.Knight (2007).
Evolutionary rates vary among rRNA structural elements.
  Nucleic Acids Res, 35, 3339-3354.  
17377584 S.Uemura, M.Dorywalska, T.H.Lee, H.D.Kim, J.D.Puglisi, and S.Chu (2007).
Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome.
  Nature, 446, 454-457.  
  17848981 S.Ueno, H.Arai, M.Suzuki, and Y.Husimi (2007).
An mRNA-protein fusion at N-terminus for evolutionary protein engineering.
  Int J Biol Sci, 3, 365-374.  
17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.
  RNA, 13, 549-554.  
17699629 T.H.Lee, S.C.Blanchard, H.D.Kim, J.D.Puglisi, and S.Chu (2007).
The role of fluctuations in tRNA selection by the ribosome.
  Proc Natl Acad Sci U S A, 104, 13661-13665.  
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
17173023 W.C.Merrick (2007).
Are we there yet?
  Nat Chem Biol, 3, 19-20.  
17203977 W.E.Running, S.Ravipaty, J.A.Karty, and J.P.Reilly (2007).
A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus.
  J Proteome Res, 6, 337-347.  
17925437 W.Li, and J.Frank (2007).
Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
  Proc Natl Acad Sci U S A, 104, 16540-16545.  
18158895 X.H.Liang, Q.Liu, and M.J.Fournier (2007).
rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity.
  Mol Cell, 28, 965-977.  
17488812 Y.Bessho, R.Shibata, S.Sekine, K.Murayama, K.Higashijima, C.Hori-Takemoto, M.Shirouzu, S.Kuramitsu, and S.Yokoyama (2007).
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
  Proc Natl Acad Sci U S A, 104, 8293-8298.
PDB codes: 1wjx 2czj
16847933 A.Aleksandrov, and T.Simonson (2006).
The tetracycline: Mg2+ complex: a molecular mechanics force field.
  J Comput Chem, 27, 1517-1533.  
16638137 A.Churkin, and D.Barash (2006).
RNAmute: RNA secondary structure mutation analysis tool.
  BMC Bioinformatics, 7, 221.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
17135184 A.Lescoute, and E.Westhof (2006).
The interaction networks of structured RNAs.
  Nucleic Acids Res, 34, 6587-6604.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
  Nucleic Acids Res, 34, 1326-1341.  
16381047 A.Ogawa, S.Sando, and Y.Aoyama (2006).
Termination-free prokaryotic protein translation by using anticodon-adjusted E. coli tRNASer as unified suppressors of the UAA/UGA/UAG stop codons. Read-through ribosome display of full-length DHFR with translated UTR as a buried spacer arm.
  Chembiochem, 7, 249-252.  
16556933 A.Pulk, U.Maiväli, and J.Remme (2006).
Identification of nucleotides in E. coli 16S rRNA essential for ribosome subunit association.
  RNA, 12, 790-796.  
16809861 A.Seshadri, and U.Varshney (2006).
Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3.
  J Biosci, 31, 281-289.  
16998486 B.S.Schuwirth, J.M.Day, C.W.Hau, G.R.Janssen, A.E.Dahlberg, J.H.Cate, and A.Vila-Sanjurjo (2006).
Structural analysis of kasugamycin inhibition of translation.
  Nat Struct Mol Biol, 13, 879-886.
PDB codes: 1vs5 1vs6 1vs7 1vs8
16786596 B.Y.Jeon, J.Jung, D.W.Kim, A.Yee, C.H.Arrowsmith, and W.Lee (2006).
Solution structure of TA1092, a ribosomal protein S24e from Thermoplasma acidophilum.
  Proteins, 64, 1095-1097.
PDB code: 2g1d
16632247 C.A.Townsend, J.M.Crawford, and T.Bililign (2006).
New images evoke FAScinating questions.
  Chem Biol, 13, 349-351.  
16762832 C.A.Woolhead, A.E.Johnson, and H.D.Bernstein (2006).
Translation arrest requires two-way communication between a nascent polypeptide and the ribosome.
  Mol Cell, 22, 587-598.  
16929303 C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, and R.Beckmann (2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
  Nature, 443, 663-668.
PDB codes: 2iw3 2iwh 2ix3 2ix8
17129165 C.Hyeon, R.I.Dima, and D.Thirumalai (2006).
Size, shape, and flexibility of RNA structures.
  J Chem Phys, 125, 194905.  
17001100 C.Romier, M.Ben Jelloul, S.Albeck, G.Buchwald, D.Busso, P.H.Celie, E.Christodoulou, V.De Marco, S.van Gerwen, P.Knipscheer, J.H.Lebbink, V.Notenboom, A.Poterszman, N.Rochel, S.X.Cohen, T.Unger, J.L.Sussman, D.Moras, T.K.Sixma, and A.Perrakis (2006).
Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies.
  Acta Crystallogr D Biol Crystallogr, 62, 1232-1242.  
16711863 C.Y.Lee (2006).
Mass fractal dimension of the ribosome and implication of its dynamic characteristics.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 042901.  
16581790 D.E.Andreev, I.M.Terenin, Y.E.Dunaevsky, S.E.Dmitriev, and I.N.Shatsky (2006).
A leaderless mRNA can bind to mammalian 80S ribosomes and direct polypeptide synthesis in the absence of translation initiation factors.
  Mol Cell Biol, 26, 3164-3169.  
16532005 D.Pan, S.Kirillov, C.M.Zhang, Y.M.Hou, and B.S.Cooperman (2006).
Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA.
  Nat Struct Mol Biol, 13, 354-359.  
17040491 D.Qiu, P.Parada, A.G.Marcos, D.Cárdenas, M.Remacha, and J.P.Ballesta (2006).
Different roles of P1 and P2 Saccharomyces cerevisiae ribosomal stalk proteins revealed by cross-linking.
  Mol Microbiol, 62, 1191-1202.  
17053098 D.Shcherbakov, M.Dontsova, M.Tribus, M.Garber, and W.Piendl (2006).
Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.
  Nucleic Acids Res, 34, 5800-5814.  
16845037 E.Bindewald, T.D.Schneider, and B.A.Shapiro (2006).
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
  Nucleic Acids Res, 34, W405-W411.  
16490268 E.C.Böttger (2006).
The ribosome as a drug target.
  Trends Biotechnol, 24, 145-147.  
16381838 E.S.Andersen, M.A.Rosenblad, N.Larsen, J.C.Westergaard, J.Burks, I.K.Wower, J.Wower, J.Gorodkin, T.Samuelsson, and C.Zwieb (2006).
The tmRDB and SRPDB resources.
  Nucleic Acids Res, 34, D163-D168.  
16698544 F.Rázga, M.Zacharias, K.Réblová, J.Koca, and J.Sponer (2006).
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.
  Structure, 14, 825-835.  
16998488 F.Schluenzen, C.Takemoto, D.N.Wilson, T.Kaminishi, J.M.Harms, K.Hanawa-Suetsugu, W.Szaflarski, M.Kawazoe, M.Shirouzu, M.Shirouzo, K.H.Nierhaus, S.Yokoyama, and P.Fucini (2006).
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
  Nat Struct Mol Biol, 13, 871-878.
PDB code: 2hhh
16689630 F.Tama, and C.L.Brooks (2006).
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.
  Annu Rev Biophys Biomol Struct, 35, 115-133.  
16547061 G.Akanuma, H.Nanamiya, Y.Natori, N.Nomura, and F.Kawamura (2006).
Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis.
  J Bacteriol, 188, 2715-2720.  
16487710 G.Hirokawa, N.Demeshkina, N.Iwakura, H.Kaji, and A.Kaji (2006).
The ribosome-recycling step: consensus or controversy?
  Trends Biochem Sci, 31, 143-149.  
16431987 G.N.Basturea, K.E.Rudd, and M.P.Deutscher (2006).
Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family.
  RNA, 12, 426-434.  
16773394 G.Papadopoulos, S.Grudinin, D.L.Kalpaxis, and T.Choli-Papadopoulou (2006).
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
  Eur Biophys J, 35, 675-683.  
17051149 G.Yusupova, L.Jenner, B.Rees, D.Moras, and M.Yusupov (2006).
Structural basis for messenger RNA movement on the ribosome.
  Nature, 444, 391-394.
PDB codes: 2hgi 2hgj 2hgp 2hgq 2hgr 2hgu
16815893 H.Gohlke, and M.F.Thorpe (2006).
A natural coarse graining for simulating large biomolecular motion.
  Biophys J, 91, 2115-2120.  
16717405 H.Yoneyama, and R.Katsumata (2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
  Biosci Biotechnol Biochem, 70, 1060-1075.  
16973438 I.K.Ali, L.Lancaster, J.Feinberg, S.Joseph, and H.F.Noller (2006).
Deletion of a conserved, central ribosomal intersubunit RNA bridge.
  Mol Cell, 23, 865-874.  
16799464 I.Wohlgemuth, M.Beringer, and M.V.Rodnina (2006).
Rapid peptide bond formation on isolated 50S ribosomal subunits.
  EMBO Rep, 7, 699-703.  
16553873 J.Dresios, P.Panopoulos, and D.Synetos (2006).
Eukaryotic ribosomal proteins lacking a eubacterial counterpart: important players in ribosomal function.
  Mol Microbiol, 59, 1651-1663.  
16972151 J.Hury, U.Nagaswamy, M.Larios-Sanz, and G.E.Fox (2006).
Ribosome origins: the relative age of 23S rRNA Domains.
  Orig Life Evol Biosph, 36, 421-429.  
17069639 J.J.Gillespie, J.S.Johnston, J.J.Cannone, and R.R.Gutell (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
  Insect Mol Biol, 15, 657-686.  
16473853 J.R.Buchan, L.S.Aucott, and I.Stansfield (2006).
tRNA properties help shape codon pair preferences in open reading frames.
  Nucleic Acids Res, 34, 1015-1027.  
16489185 J.S.Feinberg, and S.Joseph (2006).
Ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of P-site tRNA are not essential for EF-G catalyzed translocation.
  RNA, 12, 580-588.  
17124290 J.S.Pfingsten, D.A.Costantino, and J.S.Kieft (2006).
Structural basis for ribosome recruitment and manipulation by a viral IRES RNA.
  Science, 314, 1450-1454.
PDB code: 2il9
16904339 J.W.Kieltyka, and C.S.Chow (2006).
Probing RNA hairpins with cobalt(III)hexammine and electrospray ionization mass spectrometry.
  J Am Soc Mass Spectrom, 17, 1376-1382.  
16495476 J.Xu, M.C.Kiel, A.Golshani, J.G.Chosay, H.Aoki, and M.C.Ganoza (2006).
Molecular localization of a ribosome-dependent ATPase on Escherichia coli ribosomes.
  Nucleic Acids Res, 34, 1158-1165.  
16485038 K.Hamacher, J.Trylska, and J.A.McCammon (2006).
Dependency map of proteins in the small ribosomal subunit.
  PLoS Comput Biol, 2, e10.  
16391027 K.Kurosawa, T.Hosaka, N.Tamehiro, T.Inaoka, and K.Ochi (2006).
Improvement of alpha-amylase production by modulation of ribosomal component protein S12 in Bacillus subtilis 168.
  Appl Environ Microbiol, 72, 71-77.  
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
  Annu Rev Biophys Biomol Struct, 35, 299-317.  
16538608 K.Réblová, F.Lankas, F.Rázga, M.V.Krasovska, J.Koca, and J.Sponer (2006).
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
  Biopolymers, 82, 504-520.  
16565414 L.D.Kapp, S.E.Kolitz, and J.R.Lorsch (2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.
  RNA, 12, 751-764.  
16528757 L.M.Contreras Martínez, F.J.Martínez-Veracoechea, P.Pohkarel, A.D.Stroock, F.A.Escobedo, and M.P.DeLisa (2006).
Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study.
  Biotechnol Bioeng, 94, 105-117.  
16445759 L.Santos, and P.Zwickl (2006).
Interaction analysis of the AAA ATPase TAA43 by the bacterial two-hybrid system.
  FEMS Microbiol Lett, 254, 293-299.  
16407071 L.Yatime, Y.Mechulam, S.Blanquet, and E.Schmitt (2006).
Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer.
  Structure, 14, 119-128.
PDB code: 2aho
16682557 M.Bubunenko, A.Korepanov, D.L.Court, I.Jagannathan, D.Dickinson, B.R.Chaudhuri, M.B.Garber, and G.M.Culver (2006).
30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15.
  RNA, 12, 1229-1239.  
16373493 M.Khanna, H.Wu, C.Johansson, M.Caizergues-Ferrer, and J.Feigon (2006).
Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA.
  RNA, 12, 40-52.
PDB codes: 1y2y 2euy
16500956 M.Newby Lambert, E.Vöcker, S.Blumberg, S.Redemann, A.Gajraj, J.C.Meiners, and N.G.Walter (2006).
Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.
  Biophys J, 90, 3672-3685.  
17115051 M.Schüler, S.R.Connell, A.Lescoute, J.Giesebrecht, M.Dabrowski, B.Schroeer, T.Mielke, P.A.Penczek, E.Westhof, and C.M.Spahn (2006).
Structure of the ribosome-bound cricket paralysis virus IRES RNA.
  Nat Struct Mol Biol, 13, 1092-1096.
PDB code: 2noq
16619019 N.Gao, and J.Frank (2006).
A library of RNA bridges.
  Nat Chem Biol, 2, 231-232.  
17053085 N.Kirthi, B.Roy-Chaudhuri, T.Kelley, and G.M.Culver (2006).
A novel single amino acid change in small subunit ribosomal protein S5 has profound effects on translational fidelity.
  RNA, 12, 2080-2091.  
17032763 N.S.Sato, N.Hirabayashi, I.Agmon, A.Yonath, and T.Suzuki (2006).
Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center.
  Proc Natl Acad Sci U S A, 103, 15386-15391.  
16582919 O.Rackham, K.Wang, and J.W.Chin (2006).
Functional epitopes at the ribosome subunit interface.
  Nat Chem Biol, 2, 254-258.  
16648860 P.Bieling, M.Beringer, S.Adio, and M.V.Rodnina (2006).
Peptide bond formation does not involve acid-base catalysis by ribosomal residues.
  Nat Struct Mol Biol, 13, 423-428.  
17043221 P.T.Li, C.Bustamante, and I.Tinoco (2006).
Unusual mechanical stability of a minimal RNA kissing complex.
  Proc Natl Acad Sci U S A, 103, 15847-15852.  
16530169 P.Z.Qin, J.Iseri, and A.Oki (2006).
A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling.
  Biochem Biophys Res Commun, 343, 117-124.  
17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.
  Mol Cell Biol, 26, 8992-9002.  
16501572 S.Dorner, J.L.Brunelle, D.Sharma, and R.Green (2006).
The hybrid state of tRNA binding is an authentic translation elongation intermediate.
  Nat Struct Mol Biol, 13, 234-241.  
16730356 S.E.Walker, and K.Fredrick (2006).
Recognition and positioning of mRNA in the ribosome by tRNAs with expanded anticodons.
  J Mol Biol, 360, 599-609.  
16682443 T.Adilakshmi, R.A.Lease, and S.A.Woodson (2006).
Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation.
  Nucleic Acids Res, 34, e64.  
16859496 T.Hosaka, J.Xu, and K.Ochi (2006).
Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant.
  Mol Microbiol, 61, 883-897.  
17005277 T.L.Sorensen, K.E.McAuley, R.Flaig, and E.M.Duke (2006).
New light for science: synchrotron radiation in structural medicine.
  Trends Biotechnol, 24, 500-508.  
16428856 T.Matsuura, H.Tanaka, T.Matsumoto, and T.Kawai (2006).
Atomic force microscopic observation of Escherichia coli ribosomes in solution.
  Biosci Biotechnol Biochem, 70, 300-302.  
17038497 V.Berk, W.Zhang, R.D.Pai, J.H.Cate, and J.H.Cate (2006).
Structural basis for mRNA and tRNA positioning on the ribosome.
  Proc Natl Acad Sci U S A, 103, 15830-15834.
PDB codes: 2i2p 2i2t 2i2u 2i2v
16704356 W.A.Miller, and K.A.White (2006).
Long-distance RNA-RNA interactions in plant virus gene expression and replication.
  Annu Rev Phytopathol, 44, 447-467.  
16262720 A.E.Johnson (2005).
Fluorescence approaches for determining protein conformations, interactions and mechanisms at membranes.
  Traffic, 6, 1078-1092.  
16284619 A.G.Myasnikov, S.Marzi, A.Simonetti, A.M.Giuliodori, C.O.Gualerzi, G.Yusupova, M.Yusupov, and B.P.Klaholz (2005).
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.
  Nat Struct Mol Biol, 12, 1145-1149.  
16053518 A.Liiv, D.Karitkina, U.Maiväli, and J.Remme (2005).
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
  BMC Mol Biol, 6, 18.  
15876367 A.R.Cukras, and R.Green (2005).
Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
  J Mol Biol, 349, 47-59.  
16157868 A.V.Kazantsev, A.A.Krivenko, D.J.Harrington, S.R.Holbrook, P.D.Adams, and N.R.Pace (2005).
Crystal structure of a bacterial ribonuclease P RNA.
  Proc Natl Acad Sci U S A, 102, 13392-13397.
PDB code: 2a64
16269538 A.Yassin, K.Fredrick, and A.S.Mankin (2005).
Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics.
  Proc Natl Acad Sci U S A, 102, 16620-16625.  
16180279 A.Yonath (2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
  Annu Rev Biochem, 74, 649-679.  
16285924 B.A.Maguire, A.D.Beniaminov, H.Ramu, A.S.Mankin, and R.A.Zimmermann (2005).
A protein component at the heart of an RNA machine: the importance of protein l27 for the function of the bacterial ribosome.
  Mol Cell, 20, 427-435.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
16364917 B.Vestergaard, S.Sanyal, M.Roessle, L.Mora, R.H.Buckingham, J.S.Kastrup, M.Gajhede, D.I.Svergun, and M.Ehrenberg (2005).
The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure.
  Mol Cell, 20, 929-938.  
16314459 C.L.Shenvi, K.C.Dong, E.M.Friedman, J.A.Hanson, and J.H.Cate (2005).
Accessibility of 18S rRNA in human 40S subunits and 80S ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.
  RNA, 11, 1898-1908.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16257826 D.N.Wilson, and K.H.Nierhaus (2005).
Ribosomal proteins in the spotlight.
  Crit Rev Biochem Mol Biol, 40, 243-267.  
15978067 E.Evguenieva-Hackenberg (2005).
Bacterial ribosomal RNA in pieces.
  Mol Microbiol, 57, 318-325.  
15872184 F.Bélanger, G.Théberge-Julien, P.R.Cunningham, and L.Brakier-Gingras (2005).
A functional relationship between helix 1 and the 900 tetraloop of 16S ribosomal RNA within the bacterial ribosome.
  RNA, 11, 906-913.  
15722438 F.Rázga, J.Koca, J.Sponer, and N.B.Leontis (2005).
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.