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PDBsum entry 2avy

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
2avy

 

 

 

 

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Contents
Protein chains
206 a.a. *
205 a.a. *
150 a.a. *
100 a.a. *
150 a.a. *
129 a.a. *
127 a.a. *
98 a.a. *
117 a.a. *
123 a.a. *
114 a.a. *
96 a.a. *
88 a.a. *
82 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
218 a.a. *
51 a.a. *
DNA/RNA
Metals
_MG ×60
Waters ×300
* Residue conservation analysis
Obsolete entry
PDB id:
2avy
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. This file contains the 30s subunit of one 70s ribosome. The entire crystal structure contains two 70s ribosomes and is described in remark 400.
Structure: 16s ribosomal RNA. Chain: a. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5. Chain: e. 30s ribosomal protein s6.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Biol. unit: 21mer (from PQS)
Resolution:
3.46Å     R-factor:   0.279     R-free:   0.331
Authors: B.S.Schuwirth,M.A.Borovinskaya,C.W.Hau,W.Zhang,A.Vila-Sanjurjo, J.M.Holton,J.H.D.Cate
Key ref:
B.S.Schuwirth et al. (2005). Structures of the bacterial ribosome at 3.5 A resolution. Science, 310, 827-834. PubMed id: 16272117 DOI: 10.1126/science.1117230
Date:
30-Aug-05     Release date:   08-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3 from Escherichia coli (strain K12)
Seq:
Struc:
233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4 from Escherichia coli (strain K12)
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5 from Escherichia coli (strain K12)
Seq:
Struc:
167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P02358  (RS6_ECOLI) -  30S ribosomal protein S6 from Escherichia coli (strain K12)
Seq:
Struc:
135 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7 from Escherichia coli (strain K12)
Seq:
Struc:
179 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8 from Escherichia coli (strain K12)
Seq:
Struc:
130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9 from Escherichia coli (strain K12)
Seq:
Struc:
130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10 from Escherichia coli (strain K12)
Seq:
Struc:
103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11 from Escherichia coli (strain K12)
Seq:
Struc:
129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12 from Escherichia coli (strain K12)
Seq:
Struc:
124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13 from Escherichia coli (strain K12)
Seq:
Struc:
118 a.a.
114 a.a.
Protein chain
P02370  (RS14_ECOLI) - 
Protein chain
P02371  (RS15_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16 from Escherichia coli (strain K12)
Seq:
Struc:
82 a.a.
82 a.a.
Protein chain
P02373  (RS17_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18 from Escherichia coli (strain K12)
Seq:
Struc:
75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19 from Escherichia coli (strain K12)
Seq:
Struc:
92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20 from Escherichia coli (strain K12)
Seq:
Struc:
87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2 from Escherichia coli (strain K12)
Seq:
Struc:
241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
P68679  (RS21_ECOLI) -  30S ribosomal protein S21 from Escherichia coli (strain K12)
Seq:
Struc:
71 a.a.
51 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chain
  U-G-A-A-G-A-G-U-U-U-G-A-U-C-A-U-G-G-C-U-C-A-G-A-U-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1530 bases

 

 
DOI no: 10.1126/science.1117230 Science 310:827-834 (2005)
PubMed id: 16272117  
 
 
Structures of the bacterial ribosome at 3.5 A resolution.
B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, J.H.Cate.
 
  ABSTRACT  
 
We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Molecular interactions in the intersubunit bridges. (A) Contact between S13 and L5 in ribosome I. (B) Contact between S13 and L5 in ribosome II. Only the C traces for the proteins are shown, because protein side chains are not clear in the electron density of either ribosome. Residues that become inaccessible to solvent (44) are indicated in orange for L5 and in yellow for S13 and S19. The direction of view is indicated in the center. (C) Molecular interactions in bridge B3. (D) Molecular interactions in bridge B7a. (E) Molecular interactions in bridge B6. Waters modeled at the interface are shown as red spheres inside the water-accessible volume, green mesh. (F) Close approach of phosphates at the subunit interface near bridge B2c. Distances (in angstroms) between phosphate oxygens are marked.
Figure 7.
Fig. 7. Intersubunit bridges B2a and B4. (A) Minor-groove interactions between H69 and h44 and h45, broken down by region. Atoms within hydrogen-bonding distance, as mentioned in the text, are connected by dashed lines. (B) Molecular interactions in bridge B4. Protein S15 in the 30S subunit is in blue, with relevant side chains in green. The interaction is viewed from the left side of Fig. 5A (left) and from the right side of Fig. 5A (right). Electron density is visible for the side chain of Arg88 (R88) in ribosome II, but not in ribosome I. Other amino acid abbreviations: I, Ile; L, Leu; V, Val; A, Ala; Q, Gln.
 
  The above figures are reprinted by permission from the AAAs: Science (2005, 310, 827-834) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23250061 W.A.Hendrickson (2013).
Evolution of diffraction methods for solving crystal structures.
  Acta Crystallogr A, 69, 51-59.  
22622583 D.J.Ramrath, H.Yamamoto, K.Rother, D.Wittek, M.Pech, T.Mielke, J.Loerke, P.Scheerer, P.Ivanov, Y.Teraoka, O.Shpanchenko, K.H.Nierhaus, and C.M.Spahn (2012).
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
  Nature, 485, 526-529.
PDB codes: 3j18 3j19
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.  
21368145 A.S.Yassin, M.E.Haque, P.P.Datta, K.Elmore, N.K.Banavali, L.L.Spremulli, and R.K.Agrawal (2011).
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
  Proc Natl Acad Sci U S A, 108, 3918-3923.
PDB codes: 3izy 3izz
20969605 A.Vendeville, D.Larivière, and E.Fourmentin (2011).
An inventory of the bacterial macromolecular components and their spatial organization.
  FEMS Microbiol Rev, 35, 395-414.  
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
  Mol Cell, 42, 367-377.  
20876687 C.Geary, A.Chworos, and L.Jaeger (2011).
Promoting RNA helical stacking via A-minor junctions.
  Nucleic Acids Res, 39, 1066-1080.  
21292166 D.Huber, N.Rajagopalan, S.Preissler, M.A.Rocco, F.Merz, G.Kramer, and B.Bukau (2011).
SecA interacts with ribosomes in order to facilitate posttranslational translocation in bacteria.
  Mol Cell, 41, 343-353.  
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.  
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
21370971 D.V.Fedyukina, and S.Cavagnero (2011).
Protein folding at the exit tunnel.
  Annu Rev Biophys, 40, 337-359.  
  21410646 F.J.Blanco, and G.Montoya (2011).
Transient DNA / RNA-protein interactions.
  FEBS J, 278, 1643-1650.  
21292164 H.Ramu, N.Vázquez-Laslop, D.Klepacki, Q.Dai, J.Piccirilli, R.Micura, and A.S.Mankin (2011).
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center.
  Mol Cell, 41, 321-330.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
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.  
21151118 L.F.Estrozi, D.Boehringer, S.O.Shan, N.Ban, and C.Schaffitzel (2011).
Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
  Nat Struct Mol Biol, 18, 88-90.
PDB code: 2xkv
21342782 L.R.Cruz-Vera, M.S.Sachs, C.L.Squires, and C.Yanofsky (2011).
Nascent polypeptide sequences that influence ribosome function.
  Curr Opin Microbiol, 14, 160-166.  
21428957 M.V.Rodnina, and W.Wintermeyer (2011).
The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.
  Biochem Soc Trans, 39, 658-662.  
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.  
21267063 S.Bhushan, T.Hoffmann, B.Seidelt, J.Frauenfeld, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2011).
SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center.
  PLoS Biol, 9, e1000581.  
21217697 S.Feng, H.Li, J.Zhao, K.Pervushin, K.Lowenhaupt, T.U.Schwartz, and P.Dröge (2011).
Alternate rRNA secondary structures as regulators of translation.
  Nat Struct Mol Biol, 18, 169-176.
PDB code: 2l54
21415317 T.L.Grove, J.S.Benner, M.I.Radle, J.H.Ahlum, B.J.Landgraf, C.Krebs, and S.J.Booker (2011).
A radically different mechanism for S-adenosylmethionine-dependent methyltransferases.
  Science, 332, 604-607.  
21365677 W.Li, L.G.Trabuco, K.Schulten, and J.Frank (2011).
Molecular dynamics of EF-G during translocation.
  Proteins, 79, 1478-1486.
PDB code: 3izp
21734708 X.Qu, J.D.Wen, L.Lancaster, H.F.Noller, C.Bustamante, and I.Tinoco (2011).
The ribosome uses two active mechanisms to unwind messenger RNA during translation.
  Nature, 475, 118-121.  
21368154 Z.Guo, M.Gibson, S.Sitha, S.Chu, and U.Mohanty (2011).
Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome.
  Proc Natl Acad Sci U S A, 108, 3947-3951.  
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
20207951 A.E.Bunner, A.H.Beck, and J.R.Williamson (2010).
Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape.
  Proc Natl Acad Sci U S A, 107, 5417-5422.  
20188109 A.E.Bunner, S.Nord, P.M.Wikström, and J.R.Williamson (2010).
The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution.
  J Mol Biol, 398, 1-7.  
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.  
20855725 B.Llano-Sotelo, J.Dunkle, D.Klepacki, W.Zhang, P.Fernandes, J.H.Cate, and A.S.Mankin (2010).
Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
  Antimicrob Agents Chemother, 54, 4961-4970.
PDB codes: 1vt2 3or9 3ora 3orb
20176963 B.Roy-Chaudhuri, N.Kirthi, and G.M.Culver (2010).
Appropriate maturation and folding of 16S rRNA during 30S subunit biogenesis are critical for translational fidelity.
  Proc Natl Acad Sci U S A, 107, 4567-4572.  
20541504 B.Sander, M.M.Golas, R.Lührmann, and H.Stark (2010).
An approach for de novo structure determination of dynamic molecular assemblies by electron cryomicroscopy.
  Structure, 18, 667-676.  
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.  
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
20236470 E.Westhof (2010).
The amazing world of bacterial structured RNAs.
  Genome Biol, 11, 108.  
20797628 F.Brandt, L.A.Carlson, F.U.Hartl, W.Baumeister, and K.Grünewald (2010).
The three-dimensional organization of polyribosomes in intact human cells.
  Mol Cell, 39, 560-569.  
20403329 G.Cannarozzi, G.Cannarrozzi, N.N.Schraudolph, M.Faty, P.von Rohr, M.T.Friberg, A.C.Roth, P.Gonnet, G.Gonnet, and Y.Barral (2010).
A role for codon order in translation dynamics.
  Cell, 141, 355-367.  
20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
Structural signatures of antibiotic binding sites on the ribosome.
  Nucleic Acids Res, 38, 5982-5994.  
20208344 H.Nanamiya, and F.Kawamura (2010).
Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis.
  Biosci Biotechnol Biochem, 74, 451-461.  
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.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20876128 J.A.Dunkle, L.Xiong, A.S.Mankin, and J.H.Cate (2010).
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
  Proc Natl Acad Sci U S A, 107, 17152-17157.
PDB codes: 3oaq 3oar 3oas 3oat 3ofa 3ofb 3ofc 3ofd 3ofo 3ofp 3ofq 3ofr 3ofx 3ofy 3ofz 3og0
21057527 J.B.Munro, M.R.Wasserman, R.B.Altman, L.Wang, and S.C.Blanchard (2010).
Correlated conformational events in EF-G and the ribosome regulate translocation.
  Nat Struct Mol Biol, 17, 1470-1477.  
20018653 J.B.Munro, R.B.Altman, C.S.Tung, J.H.Cate, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
Spontaneous formation of the unlocked state of the ribosome is a multistep process.
  Proc Natl Acad Sci U S A, 107, 709-714.  
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.  
20940705 J.Fu, Y.Hashem, I.Wower, J.Lei, H.Y.Liao, C.Zwieb, J.Wower, and J.Frank (2010).
Visualizing the transfer-messenger RNA as the ribosome resumes translation.
  EMBO J, 29, 3819-3825.
PDB code: 3iz4
20733057 J.O.Ortiz, F.Brandt, V.R.Matias, L.Sennels, J.Rappsilber, S.H.Scheres, M.Eibauer, F.U.Hartl, and W.Baumeister (2010).
Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ.
  J Cell Biol, 190, 613-621.  
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 codes: 3izb 3izc 3izd 3ize 3izf 3izs
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.  
20110252 J.Wang, T.M.Henkin, and E.P.Nikonowicz (2010).
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.
  Nucleic Acids Res, 38, 3388-3398.
PDB code: 2khy
20211929 J.Y.Dutheil, F.Jossinet, and E.Westhof (2010).
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
  Mol Biol Evol, 27, 1868-1876.  
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.  
20038632 M.G.Gagnon, and S.V.Steinberg (2010).
The adenosine wedge: a new structural motif in ribosomal RNA.
  RNA, 16, 375-381.  
20139416 M.G.Gagnon, Y.I.Boutorine, and S.V.Steinberg (2010).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
  Nucleic Acids Res, 38, 3441-3453.  
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.  
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.  
20338515 M.Wieland, B.Berschneider, M.D.Erlacher, and J.S.Hartig (2010).
Aptazyme-mediated regulation of 16S ribosomal RNA.
  Chem Biol, 17, 236-242.  
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.  
20194115 N.Husain, K.L.Tkaczuk, S.R.Tulsidas, K.H.Kaminska, S.Cubrilo, G.Maravić-Vlahovicek, J.M.Bujnicki, and J.Sivaraman (2010).
Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.
  Nucleic Acids Res, 38, 4120-4132.
PDB codes: 3lcu 3lcv
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
20929913 R.R.Rahrig, N.B.Leontis, and C.L.Zirbel (2010).
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
  Bioinformatics, 26, 2689-2697.  
20139981 S.Bhushan, M.Gartmann, M.Halic, J.P.Armache, A.Jarasch, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
  Nat Struct Mol Biol, 17, 313-317.  
20215440 S.M.Dibrov, J.Parsons, and T.Hermann (2010).
A model for the study of ligand binding to the ribosomal RNA helix h44.
  Nucleic Acids Res, 38, 4458-4465.
PDB code: 3loa
20022945 T.Yamamoto, Y.Shimizu, T.Ueda, and Y.Shiro (2010).
Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
  J Biol Chem, 285, 5646-5652.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
20151411 X.Ge, and B.Roux (2010).
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
  J Mol Recognit, 23, 128-141.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19706509 A.C.Lamanna, and K.Karbstein (2009).
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
  Proc Natl Acad Sci U S A, 106, 14259-14264.  
19596816 A.D.Kauffmann, R.J.Campagna, C.B.Bartels, and J.L.Childs-Disney (2009).
Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.
  Nucleic Acids Res, 37, e121.  
19559090 A.E.Bunner, and J.R.Williamson (2009).
Stable isotope pulse-chase monitored by quantitative mass spectrometry applied to E. coli 30S ribosome assembly kinetics.
  Methods, 49, 136-141.  
19363026 A.J.Cork, S.Jergic, S.Hammerschmidt, B.Kobe, V.Pancholi, J.L.Benesch, C.V.Robinson, N.E.Dixon, J.A.Aquilina, and M.J.Walker (2009).
Defining the structural basis of human plasminogen binding by streptococcal surface enolase.
  J Biol Chem, 284, 17129-17137.  
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.  
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.  
19576904 B.Llano-Sotelo, D.Klepacki, and A.S.Mankin (2009).
Selection of small peptides, inhibitors of translation.
  J Mol Biol, 391, 813-819.  
19528080 C.L.Zirbel, J.E.Sponer, J.Sponer, J.Stombaugh, and N.B.Leontis (2009).
Classification and energetics of the base-phosphate interactions in RNA.
  Nucleic Acids Res, 37, 4898-4918.  
19278652 C.Tu, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2009).
Structural basis for binding of RNA and cofactor by a KsgA methyltransferase.
  Structure, 17, 374-385.
PDB codes: 3ftc 3ftd 3fte 3ftf
20004159 C.W.Carter (2009).
E pluribus tres: the 2009 nobel prize in chemistry.
  Structure, 17, 1558-1561.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19190093 D.L.Bellur, and S.A.Woodson (2009).
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly.
  Nucleic Acids Res, 37, 1886-1896.  
19213046 D.M.Hamburg, M.J.Suh, and P.A.Limbach (2009).
Limited proteolysis analysis of the ribosome is affected by subunit association.
  Biopolymers, 91, 410-422.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19154330 D.Qin, and K.Fredrick (2009).
Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA.
  Mol Microbiol, 71, 1239-1249.  
19150357 E.J.Diner, and C.S.Hayes (2009).
Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics.
  J Mol Biol, 386, 300-315.  
19400805 E.Purta, M.O'Connor, J.M.Bujnicki, and S.Douthwaite (2009).
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.
  Mol Microbiol, 72, 1147-1158.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19167328 F.Brandt, S.A.Etchells, J.O.Ortiz, A.H.Elcock, F.U.Hartl, and W.Baumeister (2009).
The native 3D organization of bacterial polysomes.
  Cell, 136, 261-271.  
19485416 G.Chen, S.D.Kennedy, and D.H.Turner (2009).
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.
  Biochemistry, 48, 5738-5752.  
19362093 G.Gürel, G.Blaha, P.B.Moore, and T.A.Steitz (2009).
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
  J Mol Biol, 389, 146-156.
PDB codes: 3g4s 3g6e 3g71
19491936 G.Kramer, D.Boehringer, N.Ban, and B.Bukau (2009).
The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins.
  Nat Struct Mol Biol, 16, 589-597.  
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.  
19366171 H.Qin, C.Grigoriadou, and B.S.Cooperman (2009).
Interaction of IF2 with the ribosomal GTPase-associated center during 70S initiation complex formation.
  Biochemistry, 48, 4699-4706.  
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.  
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.  
19240325 J.M.Holton (2009).
A beginner's guide to radiation damage.
  J Synchrotron Radiat, 16, 133-142.  
19569194 J.P.Ellis, P.H.Culviner, and S.Cavagnero (2009).
Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions.
  Protein Sci, 18, 2003-2015.  
19240142 J.Stombaugh, C.L.Zirbel, E.Westhof, and N.B.Leontis (2009).
Frequency and isostericity of RNA base pairs.
  Nucleic Acids Res, 37, 2294-2312.  
  19478915 J.Wang, I.Dasgupta, and G.E.Fox (2009).
Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters.
  Archaea, 2, 241-251.  
19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.
  Nature, 457, 977-980.  
19376708 K.Connolly, and G.Culver (2009).
Deconstructing ribosome construction.
  Trends Biochem Sci, 34, 256-263.  
19560426 K.Kitahara, and T.Suzuki (2009).
The ordered transcription of RNA domains is not essential for ribosome biogenesis in Escherichia coli.
  Mol Cell, 34, 760-766.  
19082014 K.Rijal, and C.S.Chow (2009).
A new role for cisplatin: probing ribosomal RNA structure.
  Chem Commun (Camb), (), 107-109.  
19154331 K.S.Long, J.Poehlsgaard, L.H.Hansen, S.N.Hobbie, E.C.Böttger, and B.Vester (2009).
Single 23S rRNA mutations at the ribosomal peptidyl transferase centre confer resistance to valnemulin and other antibiotics in Mycobacterium smegmatis by perturbation of the drug binding pocket.
  Mol Microbiol, 71, 1218-1227.  
19783814 K.T.Schroeder, and D.M.Lilley (2009).
Ion-induced folding of a kink turn that departs from the conventional sequence.
  Nucleic Acids Res, 37, 7281-7289.  
19324965 M.A.Zundel, G.N.Basturea, and M.P.Deutscher (2009).
Initiation of ribosome degradation during starvation in Escherichia coli.
  RNA, 15, 977-983.  
19274099 M.Aivaliotis, B.Macek, F.Gnad, P.Reichelt, M.Mann, and D.Oesterhelt (2009).
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life.
  PLoS ONE, 4, e4777.  
19625386 M.H.Mazauric, J.L.Leroy, K.Visscher, S.Yoshizawa, and D.Fourmy (2009).
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
  RNA, 15, 1775-1786.  
19645415 M.Li, A.C.Duc, E.Klosi, S.Pattabiraman, M.R.Spaller, and C.S.Chow (2009).
Selection of peptides that target the aminoacyl-tRNA site of bacterial 16S ribosomal RNA.
  Biochemistry, 48, 8299-8311.  
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
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.  
19416066 M.T.Sykes, and J.R.Williamson (2009).
A complex assembly landscape for the 30S ribosomal subunit.
  Annu Rev Biophys, 38, 197-215.  
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.  
19343072 P.Ramaswamy, and S.A.Woodson (2009).
S16 throws a conformational switch during assembly of 30S 5' domain.
  Nat Struct Mol Biol, 16, 438-445.  
19616559 P.Ramaswamy, and S.A.Woodson (2009).
Global stabilization of rRNA structure by ribosomal proteins S4, S17, and S20.
  J Mol Biol, 392, 666-677.  
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.  
19294348 Q.Wu, L.Huang, and Y.Zhang (2009).
The structure and function of catalytic RNAs.
  Sci China C Life Sci, 52, 232-244.  
19575570 R.A.Britton (2009).
Role of GTPases in bacterial ribosome assembly.
  Annu Rev Microbiol, 63, 155-176.  
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.  
19450532 R.Kohler, D.Boehringer, B.Greber, R.Bingel-Erlenmeyer, I.Collinson, C.Schaffitzel, and N.Ban (2009).
YidC and Oxa1 form dimeric insertion pores on the translating ribosome.
  Mol Cell, 34, 344-353.  
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.  
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.  
19417061 S.Shoji, N.M.Abdi, R.Bundschuh, and K.Fredrick (2009).
Contribution of ribosomal residues to P-site tRNA binding.
  Nucleic Acids Res, 37, 4033-4042.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19966413 T.J.McLellan, E.S.Marr, L.M.Wondrack, T.A.Subashi, P.A.Aeed, S.Han, Z.Xu, I.K.Wang, and B.A.Maguire (2009).
A systematic study of 50S ribosomal subunit purification enabling robust crystallization.
  Acta Crystallogr D Biol Crystallogr, 65, 1270-1282.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
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.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
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.  
19292477 X.P.Li, J.C.Chiou, M.Remacha, J.P.Ballesta, and N.E.Tumer (2009).
A two-step binding model proposed for the electrostatic interactions of ricin a chain with ribosomes.
  Biochemistry, 48, 3853-3863.  
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.  
19154332 Y.Redko, and C.Condon (2009).
Ribosomal protein L3 bound to 23S precursor rRNA stimulates its maturation by Mini-III ribonuclease.
  Mol Microbiol, 71, 1145-1154.  
19399222 Y.Timsit, Z.Acosta, F.Allemand, C.Chiaruttini, and M.Springer (2009).
The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 s ribosomal subunit assembly.
  Int J Mol Sci, 10, 817-834.  
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.  
18948294 Z.M.Lee, C.Bussema, and T.M.Schmidt (2009).
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea.
  Nucleic Acids Res, 37, D489-D493.  
18718926 A.A.Frazer-Abel, and P.J.Hagerman (2008).
Core flexibility of a truncated metazoan mitochondrial tRNA.
  Nucleic Acids Res, 36, 5472-5481.  
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.  
18096629 A.García-Marcos, S.A.Sánchez, P.Parada, J.Eid, D.M.Jameson, M.Remacha, E.Gratton, and J.P.Ballesta (2008).
Yeast ribosomal stalk heterogeneity in vivo shown by two-photon FCS and molecular brightness analysis.
  Biophys J, 94, 2884-2890.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18538662 A.L.Mallam, S.C.Onuoha, J.G.Grossmann, and S.E.Jackson (2008).
Knotted fusion proteins reveal unexpected possibilities in protein folding.
  Mol Cell, 30, 642-648.  
18832371 A.Meskauskas, and J.D.Dinman (2008).
Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.
  Nucleic Acids Res, 36, 6175-6186.  
18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
  Nucleic Acids Res, 36, 6187-6198.  
18729108 B.Lippert (2008).
Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry.
  Chem Biodivers, 5, 1455-1474.  
19098107 C.Davidovich, A.Bashan, and A.Yonath (2008).
Structural basis for cross-resistance to ribosomal PTC antibiotics.
  Proc Natl Acad Sci U S A, 105, 20665-20670.  
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.  
18757750 D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, and P.Fucini (2008).
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
  Proc Natl Acad Sci U S A, 105, 13339-13344.
PDB code: 3dll
18824514 D.Rodriguez-Correa, and A.E.Dahlberg (2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
  RNA, 14, 2314-2318.  
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.  
18497744 F.Merz, D.Boehringer, C.Schaffitzel, S.Preissler, A.Hoffmann, T.Maier, A.Rutkowska, J.Lozza, N.Ban, B.Bukau, and E.Deuerling (2008).
Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
  EMBO J, 27, 1622-1632.
PDB code: 2vrh
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.  
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.  
19019145 J.C.Chiou, X.P.Li, M.Remacha, J.P.Ballesta, and N.E.Tumer (2008).
The ribosomal stalk is required for ribosome binding, depurination of the rRNA and cytotoxicity of ricin A chain in Saccharomyces cerevisiae.
  Mol Microbiol, 70, 1441-1452.  
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.  
18708582 J.Dong, J.S.Nanda, H.Rahman, M.R.Pruitt, B.S.Shin, C.M.Wong, J.R.Lorsch, and A.G.Hinnebusch (2008).
Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNA(Met) and AUG selection.
  Genes Dev, 22, 2242-2255.  
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.  
18022640 J.K.Hilmer, A.Zlotnick, and B.Bothner (2008).
Conformational equilibria and rates of localized motion within hepatitis B virus capsids.
  J Mol Biol, 375, 581-594.  
18606549 J.LeBarron, R.A.Grassucci, T.R.Shaikh, W.T.Baxter, J.Sengupta, and J.Frank (2008).
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
  J Struct Biol, 164, 24-32.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
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.  
  18717565 J.P.Ellis, C.K.Bakke, R.N.Kirchdoerfer, L.M.Jungbauer, and S.Cavagnero (2008).
Chain dynamics of nascent polypeptides emerging from the ribosome.
  ACS Chem Biol, 3, 555-566.  
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.  
18838596 K.J.Shaw, S.Poppe, R.Schaadt, V.Brown-Driver, J.Finn, C.M.Pillar, D.Shinabarger, and G.Zurenko (2008).
In vitro activity of TR-700, the antibacterial moiety of the prodrug TR-701, against linezolid-resistant strains.
  Antimicrob Agents Chemother, 52, 4442-4447.  
19079550 K.N.Rao, S.K.Burley, and S.Swaminathan (2008).
UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
  PLoS ONE, 3, e3903.
PDB codes: 2nrq 2nwu 2ogk 2pzz
18462672 L.G.Trabuco, E.Villa, K.Mitra, J.Frank, and K.Schulten (2008).
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
  Structure, 16, 673-683.  
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.  
18625613 L.James, and B.Sargueil (2008).
RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region.
  Nucleic Acids Res, 36, 4653-4666.  
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.  
18155048 L.M.Dutca, and G.M.Culver (2008).
Assembly of the 5' and 3' minor domains of 16S ribosomal RNA as monitored by tethered probing from ribosomal protein S20.
  J Mol Biol, 376, 92.  
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
18586934 M.G.Lawrence, L.Lindahl, and J.M.Zengel (2008).
Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel.
  J Bacteriol, 190, 5862-5869.  
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
18193063 M.Rogalski, D.Karcher, and R.Bock (2008).
Superwobbling facilitates translation with reduced tRNA sets.
  Nat Struct Mol Biol, 15, 192-198.  
17694311 M.Sarver, C.L.Zirbel, J.Stombaugh, A.Mokdad, and N.B.Leontis (2008).
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
  J Math Biol, 56, 215-252.  
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.  
18772887 N.M.Wills, M.O'Connor, C.C.Nelson, C.C.Rettberg, W.M.Huang, R.F.Gesteland, and J.F.Atkins (2008).
Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA.
  EMBO J, 27, 2533-2544.  
18439898 N.Vazquez-Laslop, C.Thum, and A.S.Mankin (2008).
Molecular mechanism of drug-dependent ribosome stalling.
  Mol Cell, 30, 190-202.  
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, 046005.  
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
18946046 P.M.Petrone, C.D.Snow, D.Lucent, and V.S.Pande (2008).
Side-chain recognition and gating in the ribosome exit tunnel.
  Proc Natl Acad Sci U S A, 105, 16549-16554.  
18772248 P.S.Pallan, C.Kreutz, S.Bosio, R.Micura, and M.Egli (2008).
Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs.
  RNA, 14, 2125-2135.
PDB code: 3cjz
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.  
18288106 R.Bingel-Erlenmeyer, R.Kohler, G.Kramer, A.Sandikci, S.Antolić, T.Maier, C.Schaffitzel, B.Wiedmann, B.Bukau, and N.Ban (2008).
A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.
  Nature, 452, 108-111.
PDB codes: 2vhm 2vhn 2vho 2vhp
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.  
18566829 R.F.Degenhardt, and P.C.Bonham-Smith (2008).
Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog.
  Planta, 228, 627-640.  
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.  
19015512 S.D.Moore, and R.T.Sauer (2008).
Revisiting the mechanism of macrolide-antibiotic resistance mediated by ribosomal protein L22.
  Proc Natl Acad Sci U S A, 105, 18261-18266.  
18459975 S.Guermazi, P.Daegelen, C.Dauga, D.Rivière, T.Bouchez, J.J.Godon, G.Gyapay, A.Sghir, E.Pelletier, J.Weissenbach, and D.Le Paslier (2008).
Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach.
  Environ Microbiol, 10, 2111-2123.  
18805697 S.K.Mahto, and C.S.Chow (2008).
Synthesis and solution conformation studies of the modified nucleoside N(4),2'-O-dimethylcytidine (m(4)Cm) and its analogues.
  Bioorg Med Chem, 16, 8795-8800.  
18025251 S.M.Toh, L.Xiong, T.Bae, and A.S.Mankin (2008).
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA.
  RNA, 14, 98.  
18953726 S.Marzi, P.Fechter, C.Chevalier, P.Romby, and T.Geissmann (2008).
RNA switches regulate initiation of translation in bacteria.
  Biol Chem, 389, 585-598.  
18320553 S.Pourshahian, and P.A.Limbach (2008).
Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry.
  J Mass Spectrom, 43, 1081-1088.  
18573090 S.R.Holbrook (2008).
Structural principles from large RNAs.
  Annu Rev Biophys, 37, 445-464.  
18230758 S.Smit, K.Rother, J.Heringa, and R.Knight (2008).
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
  RNA, 14, 410-416.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
18784650 T.Adilakshmi, D.L.Bellur, and S.A.Woodson (2008).
Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly.
  Nature, 455, 1268-1272.  
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.  
18252772 T.Miyoshi, and T.Uchiumi (2008).
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
  Nucleic Acids Res, 36, 1783-1791.  
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.  
18456707 T.Yokoyama, and T.Suzuki (2008).
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
  Nucleic Acids Res, 36, 3539-3551.  
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
18658118 W.Rypniewski, D.A.Adamiak, J.Milecki, and R.W.Adamiak (2008).
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
  RNA, 14, 1845-1851.
PDB codes: 3czw 3d0m
19081053 W.Zhang, M.Kimmel, C.M.Spahn, and P.A.Penczek (2008).
Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis.
  Structure, 16, 1770-1776.  
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.
  Mol Cell, 32, 190-197.  
19111659 X.Luo, H.H.Hsiao, M.Bubunenko, G.Weber, D.L.Court, M.E.Gottesman, H.Urlaub, and M.C.Wahl (2008).
Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
  Mol Cell, 32, 791-802.
PDB codes: 3d3b 3d3c
18391965 Z.Xu, H.C.O'Farrell, J.P.Rife, and G.M.Culver (2008).
A conserved rRNA methyltransferase regulates ribosome biogenesis.
  Nat Struct Mol Biol, 15, 534-536.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
  J Mol Biol, 373, 1058-1070.  
17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
  Trends Biochem Sci, 32, 434-441.  
17940016 A.Korostelev, S.Trakhanov, H.Asahara, M.Laurberg, L.Lancaster, and H.F.Noller (2007).
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
  Proc Natl Acad Sci U S A, 104, 16840-16843.
PDB codes: 1vsp 2qnh
17683199 A.L.Manuell, J.Quispe, and S.P.Mayfield (2007).
Structure of the chloroplast ribosome: novel domains for translation regulation.
  PLoS Biol, 5, e209.  
17386264 A.Meskauskas, and J.D.Dinman (2007).
Ribosomal protein L3: gatekeeper to the A site.
  Mol Cell, 25, 877-888.  
17568775 A.Unbehaun, A.Marintchev, I.B.Lomakin, T.Didenko, G.Wagner, C.U.Hellen, and T.V.Pestova (2007).
Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing.
  EMBO J, 26, 3109-3123.  
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
17848413 B.W.Ying, D.Fourmy, and S.Yoshizawa (2007).
Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA.
  RNA, 13, 2042-2050.  
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.
  Mol Cell, 27, 250-261.  
17360517 C.Davidovich, A.Bashan, T.Auerbach-Nevo, R.D.Yaggie, R.R.Gontarek, and A.Yonath (2007).
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
  Proc Natl Acad Sci U S A, 104, 4291-4296.
PDB codes: 2ogm 2ogn 2ogo
17881742 C.Guarraia, L.Norris, A.Raman, and P.J.Farabaugh (2007).
Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon.
  RNA, 13, 1940-1947.  
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.  
17128284 C.S.Fraser, and J.A.Doudna (2007).
Structural and mechanistic insights into hepatitis C viral translation initiation.
  Nat Rev Microbiol, 5, 29-38.  
17601995 C.Yanofsky (2007).
RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria.
  RNA, 13, 1141-1154.  
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
17283215 D.Piekna-Przybylska, W.A.Decatur, and M.J.Fournier (2007).
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.
  RNA, 13, 305-312.  
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.  
17439971 F.Allemand, J.Haentjens, C.Chiaruttini, C.Royer, and M.Springer (2007).
Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites.
  Nucleic Acids Res, 35, 3016-3031.  
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.  
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.  
17272297 G.Zoldák, L.Redecke, D.I.Svergun, P.V.Konarev, C.S.Voertler, H.Dobbek, E.Sedlák, and M.Sprinzl (2007).
Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies.
  Nucleic Acids Res, 35, 1343-1353.
PDB code: 2ihr
17540173 H.Gao, Z.Zhou, U.Rawat, C.Huang, L.Bouakaz, C.Wang, Z.Cheng, Y.Liu, A.Zavialov, R.Gursky, S.Sanyal, M.Ehrenberg, J.Frank, and H.Song (2007).
RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.
  Cell, 129, 929-941.
PDB codes: 2h5e 2o0f
17905831 H.K.Lamb, P.Thompson, C.Elliott, I.G.Charles, J.Richards, M.Lockyer, N.Watkins, C.Nichols, D.K.Stammers, C.R.Bagshaw, A.Cooper, and A.R.Hawkins (2007).
Functional analysis of the GTPases EngA and YhbZ encoded by Salmonella typhimurium.
  Protein Sci, 16, 2391-2402.  
17895397 H.Li, R.Liang, D.H.Turner, L.J.Rothberg, and S.Duan (2007).
Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.
  RNA, 13, 2034-2041.  
17320904 H.Pan, J.D.Ho, R.M.Stroud, and J.Finer-Moore (2007).
The crystal structure of E. coli rRNA pseudouridine synthase RluE.
  J Mol Biol, 367, 1459-1470.
PDB codes: 2olw 2oml
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 codes: 2jq7 2nyo
17317624 J.B.Munro, R.B.Altman, N.O'Connor, and S.C.Blanchard (2007).
Identification of two distinct hybrid state intermediates on the ribosome.
  Mol Cell, 25, 505-517.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
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.  
18047298 J.M.Blose, M.L.Manni, K.A.Klapec, Y.Stranger-Jones, A.C.Zyra, V.Sim, C.A.Griffith, J.D.Long, and M.J.Serra (2007).
Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.
  Biochemistry, 46, 15123-15135.  
17875999 J.Wachino, K.Shibayama, H.Kurokawa, K.Kimura, K.Yamane, S.Suzuki, N.Shibata, Y.Ike, and Y.Arakawa (2007).
Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides.
  Antimicrob Agents Chemother, 51, 4401-4409.  
17514744 K.Karbstein (2007).
Role of GTPases in ribosome assembly.
  Biopolymers, 87, 1.  
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.  
17499045 K.L.Leach, S.M.Swaney, J.R.Colca, W.G.McDonald, J.R.Blinn, L.M.Thomasco, R.C.Gadwood, D.Shinabarger, L.Xiong, and A.S.Mankin (2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
  Mol Cell, 26, 393-402.  
17704156 K.Réblová, E.Fadrná, J.Sarzynska, T.Kulinski, P.Kulhánek, E.Ennifar, J.Koca, and J.Sponer (2007).
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.
  Biophys J, 93, 3932-3949.  
17592474 K.Wang, H.Neumann, S.Y.Peak-Chew, and J.W.Chin (2007).
Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.
  Nat Biotechnol, 25, 770-777.  
17360328 L.H.Horan, and H.F.Noller (2007).
Intersubunit movement is required for ribosomal translocation.
  Proc Natl Acad Sci U S A, 104, 4881-4885.  
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.
  J Mol Biol, 368, 853-869.  
17293420 L.R.Cruz-Vera, A.New, C.Squires, and C.Yanofsky (2007).
Ribosomal features essential for tna operon induction: tryptophan binding at the peptidyl transferase center.
  J Bacteriol, 189, 3140-3146.  
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
17685395 M.A.Ditzler, E.A.Alemán, D.Rueda, and N.G.Walter (2007).
Focus on function: single molecule RNA enzymology.
  Biopolymers, 87, 302-316.  
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.  
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.  
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.  
17289755 N.Choonee, S.Even, L.Zig, and H.Putzer (2007).
Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism.
  Nucleic Acids Res, 35, 1578-1588.  
17996252 N.Gao, A.V.Zavialov, M.Ehrenberg, and J.Frank (2007).
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
  J Mol Biol, 374, 1345-1358.
PDB code: 2rdo
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.  
17389391 R.J.Gilbert, Y.Gordiyenko, T.von der Haar, A.F.Sonnen, G.Hofmann, M.Nardelli, D.I.Stuart, and J.E.McCarthy (2007).
Reconfiguration of yeast 40S ribosomal subunit domains by the translation initiation multifactor complex.
  Proc Natl Acad Sci U S A, 104, 5788-5793.  
17951333 R.L.Gonzalez, S.Chu, and J.D.Puglisi (2007).
Thiostrepton inhibition of tRNA delivery to the ribosome.
  RNA, 13, 2091-2097.  
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.  
17321546 S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, and P.B.Moore (2007).
The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
  J Mol Biol, 367, 1471-1479.
PDB codes: 2otj 2otl
17664317 S.J.Schroeder, G.Blaha, and P.B.Moore (2007).
Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
  Antimicrob Agents Chemother, 51, 4462-4465.
PDB code: 2qex
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.  
17555436 S.M.Toh, L.Xiong, C.A.Arias, M.V.Villegas, K.Lolans, J.Quinn, and A.S.Mankin (2007).
Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid.
  Mol Microbiol, 64, 1506-1514.  
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.  
17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.
  RNA, 13, 549-554.  
17507660 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
  RNA, 13, 1036-1042.  
17956547 S.Zaman, M.Fitzpatrick, L.Lindahl, and J.Zengel (2007).
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli.
  Mol Microbiol, 66, 1039-1050.  
17259282 T.Créty, and T.E.Malliavin (2007).
The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA.
  Biophys J, 92, 2647-2665.
PDB code: 2fkx
17355865 T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, and S.Yokoyama (2007).
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
  Structure, 15, 289-297.
PDB code: 2e5l
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
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.  
17572081 W.G.Scott (2007).
Ribozymes.
  Curr Opin Struct Biol, 17, 280-286.  
17872510 W.Huggins, T.Shapkina, and P.Wollenzien (2007).
Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s(4)U8-C13 photocrosslinking.
  RNA, 13, 2000-2011.  
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.  
17660743 X.Zhong, X.Tao, J.Stombaugh, N.Leontis, and B.Ding (2007).
Tertiary structure and function of an RNA motif required for plant vascular entry to initiate systemic trafficking.
  EMBO J, 26, 3836-3846.  
17616982 Z.Yao, J.Barrick, Z.Weinberg, S.Neph, R.Breaker, M.Tompa, and W.L.Ruzzo (2007).
A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes.
  PLoS Comput Biol, 3, e126.  
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.  
17021617 A.Mankin (2006).
Antibiotic blocks mRNA path on the ribosome.
  Nat Struct Mol Biol, 13, 858-860.  
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.  
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.  
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
16753066 B.Vester, L.H.Hansen, L.B.Lundberg, B.R.Babu, M.D.Sørensen, J.Wengel, and S.Douthwaite (2006).
Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets.
  BMC Mol Biol, 7, 19.  
16716074 C.Maeder, G.L.Conn, and D.E.Draper (2006).
Optimization of a ribosomal structural domain by natural selection.
  Biochemistry, 45, 6635-6643.  
17086205 C.Schaffitzel, M.Oswald, I.Berger, T.Ishikawa, J.P.Abrahams, H.K.Koerten, R.I.Koning, and N.Ban (2006).
Structure of the E. coli signal recognition particle bound to a translating ribosome.
  Nature, 444, 503-506.
PDB code: 2iy3
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.  
16959571 D.H.Broder, and K.Pogliano (2006).
Forespore engulfment mediated by a ratchet-like mechanism.
  Cell, 126, 917-928.  
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.  
16956407 D.W.Rice, and J.D.Palmer (2006).
An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters.
  BMC Biol, 4, 31.  
16490268 E.C.Böttger (2006).
The ribosome as a drug target.
  Trends Biotechnol, 24, 145-147.  
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
16478715 G.S.Couch, D.K.Hendrix, and T.E.Ferrin (2006).
Nucleic acid visualization with UCSF Chimera.
  Nucleic Acids Res, 34, e29.  
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
16713584 H.Muto, H.Nakatogawa, and K.Ito (2006).
Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall.
  Mol Cell, 22, 545-552.  
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.  
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.  
16452297 J.Kondo, A.Urzhumtsev, and E.Westhof (2006).
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
  Nucleic Acids Res, 34, 676-685.
PDB code: 2fqn
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.  
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.  
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.  
16801432 K.S.Long, J.Poehlsgaard, C.Kehrenberg, S.Schwarz, and B.Vester (2006).
The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics.
  Antimicrob Agents Chemother, 50, 2500-2505.  
16505360 L.R.Cruz-Vera, M.Gong, and C.Yanofsky (2006).
Changes produced by bound tryptophan in the ribosome peptidyl transferase center in response to TnaC, a nascent leader peptide.
  Proc Natl Acad Sci U S A, 103, 3598-3603.  
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.  
17086193 M.Halic, M.Blau, T.Becker, T.Mielke, M.R.Pool, K.Wild, I.Sinning, and R.Beckmann (2006).
Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
  Nature, 444, 507-511.
PDB codes: 2j28 2j37
16980477 M.Jiang, K.Datta, A.Walker, J.Strahler, P.Bagamasbad, P.C.Andrews, and J.R.Maddock (2006).
The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly.
  J Bacteriol, 188, 6757-6770.  
16713707 N.B.Leontis, A.Lescoute, and E.Westhof (2006).
The building blocks and motifs of RNA architecture.
  Curr Opin Struct Biol, 16, 279-287.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
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.  
16456030 N.Spacková, and J.Sponer (2006).
Molecular dynamics simulations of sarcin-ricin rRNA motif.
  Nucleic Acids Res, 34, 697-708.  
16582919 O.Rackham, K.Wang, and J.W.Chin (2006).
Functional epitopes at the ribosome subunit interface.
  Nat Chem Biol, 2, 254-258.  
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.  
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
16682558 W.Li, J.Sengupta, B.K.Rath, and J.Frank (2006).
Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations.
  RNA, 12, 1240-1253.
PDB code: 2gkz
16977336 Y.Timsit, F.Allemand, C.Chiaruttini, and M.Springer (2006).
Coexistence of two protein folding states in the crystal structure of ribosomal protein L20.
  EMBO Rep, 7, 1013-1018.
PDB code: 2ghj
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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