PDBsum entry 1ibk

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
Jmol PyMol
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. *
_MG ×113
_ZN ×2
* Residue conservation analysis
PDB id:
Name: Ribosome
Title: Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotic paromomycin
Structure: 16s ribosomal RNA. Chain: a. P-site messenger RNA fragment. Chain: x. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: 22mer (from PQS)
3.31Å     R-factor:   0.229     R-free:   0.282
Authors: J.M.Ogle,D.E.Brodersen,W.M.Clemons Jr.,M.J.Tarry,A.P.Carter, V.Ramakrishnan
Key ref:
J.M.Ogle et al. (2001). Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897-902. PubMed id: 11340196 DOI: 10.1126/science.1060612
28-Mar-01     Release date:   04-May-01    
Go to PROCHECK summary

Protein chain
No UniProt id for this chain
Struc: 234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
156 a.a.
155 a.a.
Protein chain
A0A0M9AFS9  (RS8_THEAQ) -  30S ribosomal protein S8
138 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
126 a.a.
125 a.a.
Protein chain
A0A0N0BLP2  (RS14Z_THEAQ) -  30S ribosomal protein S14 type Z
61 a.a.
60 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
88 a.a.
83 a.a.
Protein chain
A0A0N0BLS5  (RS17_THEAQ) -  30S ribosomal protein S17
105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 19 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     6 terms  


DOI no: 10.1126/science.1060612 Science 292:897-902 (2001)
PubMed id: 11340196  
Recognition of cognate transfer RNA by the 30S ribosomal subunit.
J.M.Ogle, D.E.Brodersen, W.M.Clemons, M.J.Tarry, A.P.Carter, V.Ramakrishnan.
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.
  Selected figure(s)  
Figure 2.
Fig. 2. Complex of the 30S subunit with mRNA from a U[6] hexanucleotide and a cognate tRNA-ASL. (A) Overview of the complex. The 50S interface side of the 30S subunit is facing the reader, and important elements have been given standard colors that are used throughout the figures, namely, ASL at the A site (gold), codon from the U[6] hexanucleotide at the A site (purple), 3' end of 16S RNA that mimics mRNA at the P site (green), P site tRNA mimic introduced by helix 6 from a neighboring molecule (dark blue), and protein S12 (tan). (B) Stereo view showing details of the A and P sites, colored as in (A), with, in addition, helix 44 (cyan, right), helix 34 (blue, left), 530 loop (green, left), and paromomycin (yellow sticks, within helix 44). The hydrogen bonds responsible for the codon-anticodon interaction at both the A and P sites are shown as red lines.
Figure 3.
Fig. 3. Stereo views showing interactions of the ribosome with the codon-anticodon base pairs. The tightness of the interactions is shown by the semitransparent van der Waals surface. (A) In the first position, A1493 binds in the minor groove of the A36-U1 base pair. (B) In the second position, G530 and A1492 (both brown) act in concert to monitor the A35-U2 base pair. (C) The third (wobble) position, showing the G34-U3 base pair. C1054 stacks against G36 of the ASL. U3 interacts with G530, and indirectly through a Mg2+ ion (magenta) with C518 and residue Pro48 (E. coli Pro44) from protein S12 (gray). The base pair seems closer to Watson-Crick geometry. (D) The third position in the presence of paromomycin, with the expected GU wobble pair. The interactions with the ribosome are similar to those in (C).
  The above figures are reprinted by permission from the AAAs: Science (2001, 292, 897-902) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
22437501 N.Demeshkina, L.Jenner, E.Westhof, M.Yusupov, and G.Yusupova (2012).
A new understanding of the decoding principle on the ribosome.
  Nature, 484, 256-259.
PDB codes: 3tve 3tvf 3tvg 3tvh 3uyd 3uye 3uyf 3uyg 3uz1 3uz2 3uz3 3uz4 3uz6 3uz7 3uz8 3uz9 3uzf 3uzg 3uzh 3uzi 3uzk 3uzl 3uzm 3uzn
21453453 A.B.Mentewab, M.J.Jacobsen, and R.A.Flowers (2011).
Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana.
  BMC Res Notes, 4, 93.  
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
  Biophys J, 100, 2201-2208.  
21286630 G.D.Wright (2011).
Molecular mechanisms of antibiotic resistance.
  Chem Commun (Camb), 47, 4055-4061.  
21291859 M.Ouberai, F.El Garch, A.Bussiere, M.Riou, D.Alsteens, L.Lins, I.Baussanne, Y.F.Dufrêne, R.Brasseur, J.L.Decout, and M.P.Mingeot-Leclercq (2011).
The Pseudomonas aeruginosa membranes: A target for a new amphiphilic aminoglycoside derivative?
  Biochim Biophys Acta, 1808, 1716-1727.  
22020300 P.K.Khade, and S.Joseph (2011).
Messenger RNA interactions in the decoding center control the rate of translocation.
  Nat Struct Mol Biol, 18, 1300-1302.  
21154494 T.Cottin, C.Pyrkotis, C.I.Stathakis, I.Mavridis, I.A.Katsoulis, P.Anastasopoulou, G.Kythreoti, A.L.Zografos, V.R.Nahmias, A.Papakyriakou, and D.Vourloumis (2011).
Designed spiro-bicyclic analogues targeting the ribosomal decoding center.
  Chembiochem, 12, 71-87.  
21378964 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, and V.Ramakrishnan (2011).
How mutations in tRNA distant from the anticodon affect the fidelity of decoding.
  Nat Struct Mol Biol, 18, 432-436.
PDB codes: 2y0u 2y0v 2y0w 2y0x 2y0y 2y0z 2y10 2y11 2y12 2y13 2y14 2y15 2y16 2y17 2y18 2y19
21378755 X.Agirrezabala, E.Schreiner, L.G.Trabuco, J.Lei, R.F.Ortiz-Meoz, K.Schulten, R.Green, and J.Frank (2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
  EMBO J, 30, 1497-1507.
PDB codes: 3izt 3izu 3izv 3izw
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
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
20564281 G.De Pascale, and G.D.Wright (2010).
Antibiotic resistance by enzyme inactivation: from mechanisms to solutions.
  Chembiochem, 11, 1325-1334.  
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.  
20842102 I.Wohlgemuth, C.Pohl, and M.V.Rodnina (2010).
Optimization of speed and accuracy of decoding in translation.
  EMBO J, 29, 3701-3709.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
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.  
20512119 J.Sund, M.Andér, and J.Aqvist (2010).
Principles of stop-codon reading on the ribosome.
  Nature, 465, 947-950.  
19899089 K.D.Green, W.Chen, J.L.Houghton, M.Fridman, and S.Garneau-Tsodikova (2010).
Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of N-acylated aminoglycosides.
  Chembiochem, 11, 119-126.  
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.  
20833577 M.S.Ramirez, and M.E.Tolmasky (2010).
Aminoglycoside modifying enzymes.
  Drug Resist Updat, 13, 151-171.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
19914248 P.Khade, and S.Joseph (2010).
Functional interactions by transfer RNAs in the ribosome.
  FEBS Lett, 584, 420-426.  
  20862306 P.Shah, and M.A.Gilchrist (2010).
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.
  PLoS Genet, 6, 0.  
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
21051640 R.M.Voorhees, T.M.Schmeing, A.C.Kelley, and V.Ramakrishnan (2010).
The mechanism for activation of GTP hydrolysis on the ribosome.
  Science, 330, 835-838.
PDB codes: 2xqd 2xqe
20208546 S.L.He, and R.Green (2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
  Nat Struct Mol Biol, 17, 465-470.  
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
20882682 W.E.Running, and J.P.Reilly (2010).
Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.
  Proteomics, 10, 3669-3687.  
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.  
20464029 Y.Xie, A.V.Dix, and Y.Tor (2010).
Antibiotic selectivity for prokaryotic vs. eukaryotic decoding sites.
  Chem Commun (Camb), 46, 5542-5544.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19576904 B.Llano-Sotelo, D.Klepacki, and A.S.Mankin (2009).
Selection of small peptides, inhibitors of translation.
  J Mol Biol, 391, 813-819.  
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.  
19801658 B.Pertschy, C.Schneider, M.Gnädig, T.Schäfer, D.Tollervey, and E.Hurt (2009).
RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1.
  J Biol Chem, 284, 35079-35091.  
20005802 C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, and D.E.Brodersen (2009).
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
  Cell, 139, 1084-1095.
PDB codes: 3kha 3kiq 3kir 3kis 3kit 3kiu 3kiw 3kix 3kiy
19539793 C.U.Hellen (2009).
IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry.
  Biochim Biophys Acta, 1789, 558-570.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19019162 E.Diago-Navarro, L.Mora, R.H.Buckingham, R.Díaz-Orejas, and M.Lemonnier (2009).
Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.
  Mol Microbiol, 71, 66-78.  
19861423 F.A.Vendeix, A.M.Munoz, and P.F.Agris (2009).
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.
  RNA, 15, 2278-2287.  
19216718 F.Salvatori, V.Cantale, G.Breveglieri, C.Zuccato, A.Finotti, N.Bianchi, M.Borgatti, G.Feriotto, F.Destro, A.Canella, L.Breda, S.Rivella, and R.Gambari (2009).
Development of K562 cell clones expressing beta-globin mRNA carrying the beta039 thalassaemia mutation for the screening of correctors of stop-codon mutations.
  Biotechnol Appl Biochem, 54, 41-52.  
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.  
19343177 G.Zhang, and Z.Ignatova (2009).
Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis.
  PLoS ONE, 4, e5036.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19386726 H.Vallabhaneni, and P.J.Farabaugh (2009).
Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction.
  RNA, 15, 1100-1109.  
19585638 I.A.Katsoulis, C.Pyrkotis, A.Papakyriakou, G.Kythreoti, A.L.Zografos, I.Mavridis, V.R.Nahmias, P.Anastasopoulou, and D.Vourloumis (2009).
Unnatural rigid scaffolds targeting the bacterial ribosome.
  Chembiochem, 10, 1969-1972.  
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.  
19492048 J.Lehmann, M.Cibils, and A.Libchaber (2009).
Emergence of a code in the polymerization of amino acids along RNA templates.
  PLoS One, 4, e5773.  
19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.
  Nature, 457, 977-980.  
19776006 L.E.Holberger, and C.S.Hayes (2009).
Ribosomal protein S12 and aminoglycoside antibiotics modulate A-site mRNA cleavage and transfer-messenger RNA activity in Escherichia coli.
  J Biol Chem, 284, 32188-32200.  
19239890 M.C.Wahl, C.L.Will, and R.Lührmann (2009).
The spliceosome: design principles of a dynamic RNP machine.
  Cell, 136, 701-718.  
19081939 M.J.Belousoff, B.Graham, L.Spiccia, and Y.Tor (2009).
Cleavage of RNA oligonucleotides by aminoglycosides.
  Org Biomol Chem, 7, 30-33.  
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.  
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.  
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.  
19343067 P.Schimmel, and M.Guo (2009).
A tipping point for mistranslation and disease.
  Nat Struct Mol Biol, 16, 348-349.  
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.  
19132006 S.Nonin-Lecomte, N.Germain-Amiot, R.Gillet, M.Hallier, L.Ponchon, F.Dardel, and B.Felden (2009).
Ribosome hijacking: a role for small protein B during trans-translation.
  EMBO Rep, 10, 160-165.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19095621 S.T.Gregory, J.F.Carr, and A.E.Dahlberg (2009).
A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA.
  RNA, 15, 208-214.  
19129224 T.Dale, R.P.Fahlman, M.Olejniczak, and O.C.Uhlenbeck (2009).
Specificity of the ribosomal A site for aminoacyl-tRNAs.
  Nucleic Acids Res, 37, 1202-1210.  
19833920 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, Y.G.Gao, F.V.Murphy, J.R.Weir, and V.Ramakrishnan (2009).
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
  Science, 326, 688-694.
PDB codes: 2wrn 2wro 2wrq 2wrr
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
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.  
19908830 Y.Xie, A.V.Dix, and Y.Tor (2009).
FRET enabled real time detection of RNA-small molecule binding.
  J Am Chem Soc, 131, 17605-17614.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
19064930 A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, and H.F.Noller (2008).
Crystal structure of a translation termination complex formed with release factor RF2.
  Proc Natl Acad Sci U S A, 105, 19684-19689.
PDB codes: 3f1e 3f1f 3f1g 3f1h
18988853 A.Weixlbaumer, H.Jin, C.Neubauer, R.M.Voorhees, S.Petry, A.C.Kelley, and V.Ramakrishnan (2008).
Insights into translational termination from the structure of RF2 bound to the ribosome.
  Science, 322, 953-956.
PDB codes: 2jl5 2jl6 2jl7 2jl8 2wh1 2wh2 2wh3 2wh4
18158305 C.Geary, S.Baudrey, and L.Jaeger (2008).
Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors.
  Nucleic Acids Res, 36, 1138-1152.  
18058790 D.Balenci, F.Bernardi, L.Cellai, N.D'Amelio, E.Gaggelli, N.Gaggelli, E.Molteni, and G.Valensin (2008).
Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site.
  Chembiochem, 9, 114-123.  
18377929 F.Garza-Sánchez, J.G.Gin, and C.S.Hayes (2008).
Amino acid starvation and colicin D treatment induce A-site mRNA cleavage in Escherichia coli.
  J Mol Biol, 378, 505-519.  
18667428 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine.
  J Biol Chem, 283, 26548-26556.
PDB codes: 3dmf 3dmg 3dmh
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 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.  
18094117 H.P.Harding, J.G.Lackey, H.C.Hsu, Y.Zhang, J.Deng, R.M.Xu, M.J.Damha, and D.Ron (2008).
An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation.
  RNA, 14, 225-232.  
18755843 J.E.Brock, S.Pourshahian, J.Giliberti, P.A.Limbach, and G.R.Janssen (2008).
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
  RNA, 14, 2159-2169.  
18346970 J.Kondo, and E.Westhof (2008).
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
  Nucleic Acids Res, 36, 2654-2666.
PDB codes: 3bnl 3bnn 3bno 3bnp 3bnq 3bnr 3bns 3bnt
18495942 J.Lehmann, and A.Libchaber (2008).
Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon.
  RNA, 14, 1264-1269.  
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
19343095 M.Długosz, J.M.Antosiewicz, and J.Trylska (2008).
Association of aminoglycosidic antibiotics with the ribosomal A-site studied with Brownian dynamics.
  J Chem Theory Comput, 4, 549-559.  
18174989 M.Hainrichson, I.Nudelman, and T.Baasov (2008).
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.
  Org Biomol Chem, 6, 227-239.  
18400551 M.Johansson, M.Lovmar, and M.Ehrenberg (2008).
Rate and accuracy of bacterial protein synthesis revisited.
  Curr Opin Microbiol, 11, 141-147.  
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
18590561 M.R.Miller, D.W.Healey, S.G.Robison, J.D.Dewey, and A.R.Buskirk (2008).
The role of upstream sequences in selecting the reading frame on tmRNA.
  BMC Biol, 6, 29.  
18586937 M.Savic, T.Ilic-Tomic, R.Macmaster, B.Vasiljevic, and G.L.Conn (2008).
Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm.
  J Bacteriol, 190, 5855-5861.  
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.  
18818369 M.Simonović, and T.A.Steitz (2008).
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
  RNA, 14, 2372-2378.
PDB codes: 3cma 3cme
18774127 O.J.Barrett, A.Pushechnikov, M.Wu, and M.D.Disney (2008).
Studying aminoglycoside modification by the acetyltransferase class of resistance-causing enzymes via microarray.
  Carbohydr Res, 343, 2924-2931.  
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
18552770 P.F.Agris (2008).
Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications.
  EMBO Rep, 9, 629-635.  
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.
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18614050 S.Ledoux, and O.C.Uhlenbeck (2008).
Different aa-tRNAs are selected uniformly on the ribosome.
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18308926 S.N.Hobbie, C.M.Bruell, S.Akshay, S.K.Kalapala, D.Shcherbakov, and E.C.Böttger (2008).
Mitochondrial deafness alleles confer misreading of the genetic code.
  Proc Natl Acad Sci U S A, 105, 3244-3249.  
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
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
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.
  Mol Cell, 32, 190-197.  
19088750 Y.S.Khairulina, M.V.Molotkov, K.N.Bulygin, D.M.Graifer, A.G.Ven'yaminova, L.Y.Frolova, J.Stahl, and G.G.Karpova (2008).
[Protein S3 Fragments Neighboring mRNA during Elongation and Translation Termination on the Human Ribosome.]
  Bioorg Khim, 34, 773-780.  
17244535 A.Fabbretti, C.L.Pon, S.P.Hennelly, W.E.Hill, J.S.Lodmell, and C.O.Gualerzi (2007).
The real-time path of translation factor IF3 onto and off the ribosome.
  Mol Cell, 25, 285-296.  
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.  
17956616 A.S.Novozhilov, Y.I.Wolf, and E.V.Koonin (2007).
Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.
  Biol Direct, 2, 24.  
17496902 A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.Vendeix, P.F.Agris, and V.Ramakrishnan (2007).
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines.
  Nat Struct Mol Biol, 14, 498-502.
PDB codes: 2uu9 2uua 2uub 2uuc
18431442 C.M.Barbieri, M.Kaul, and D.S.Pilch (2007).
Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site.
  Tetrahedron, 63, 3567-6574.  
17353247 C.M.Barbieri, M.Kaul, M.Bozza-Hingos, F.Zhao, Y.Tor, T.Hermann, and D.S.Pilch (2007).
Defining the molecular forces that determine the impact of neomycin on bacterial protein synthesis: importance of the 2'-amino functionality.
  Antimicrob Agents Chemother, 51, 1760-1769.  
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
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
17592040 D.L.Taliaferro, and P.J.Farabaugh (2007).
Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site.
  RNA, 13, 1279-1286.  
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.  
17967466 D.Sharma, A.R.Cukras, E.J.Rogers, D.R.Southworth, and R.Green (2007).
Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome.
  J Mol Biol, 374, 1065-1076.  
17095544 E.B.Kramer, and P.J.Farabaugh (2007).
The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.
  RNA, 13, 87-96.  
18042450 E.M.Youngman, S.L.He, L.J.Nikstad, and R.Green (2007).
Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release.
  Mol Cell, 28, 533-543.  
17565370 E.P.Plant, P.Nguyen, J.R.Russ, Y.R.Pittman, T.Nguyen, J.T.Quesinberry, T.G.Kinzy, and J.D.Dinman (2007).
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
  PLoS ONE, 2, e517.  
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.  
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
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.  
17722211 J.Kondo, K.Pachamuthu, B.François, J.Szychowski, S.Hanessian, and E.Westhof (2007).
Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity.
  ChemMedChem, 2, 1631-1638.
PDB code: 2pwt
17705310 J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, C.M.Barbieri, D.S.Pilch, E.Westhof, and T.Baasov (2007).
Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.
  Chembiochem, 8, 1700-1709.
PDB codes: 2o3v 2o3w 2o3x 2o3y
16892199 J.Zhou, G.Wang, L.H.Zhang, and X.S.Ye (2007).
Modifications of aminoglycoside antibiotics targeting RNA.
  Med Res Rev, 27, 279-316.  
17159993 L.Cochella, J.L.Brunelle, and R.Green (2007).
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.
  Nat Struct Mol Biol, 14, 30-36.  
17923669 L.Desigaux, M.Sainlos, O.Lambert, R.Chevre, E.Letrou-Bonneval, J.P.Vigneron, P.Lehn, J.M.Lehn, and B.Pitard (2007).
Self-assembled lamellar complexes of siRNA with lipidic aminoglycoside derivatives promote efficient siRNA delivery and interference.
  Proc Natl Acad Sci U S A, 104, 16534-16539.  
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.  
17186006 L.V.Zingman, S.Park, T.M.Olson, A.E.Alekseev, and A.Terzic (2007).
Aminoglycoside-induced translational read-through in disease: overcoming nonsense mutations by pharmacogenetic therapy.
  Clin Pharmacol Ther, 81, 99.  
17379816 M.E.Saks, and J.S.Conery (2007).
Anticodon-dependent conservation of bacterial tRNA gene sequences.
  RNA, 13, 651-660.  
17323326 P.C.Anderson, and S.Mecozzi (2007).
Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site A.
  Biopolymers, 86, 95.  
17115251 P.Jayaguru, and M.Raghunathan (2007).
Group I intron renders differential susceptibility of Candida albicans to Bleomycin.
  Mol Biol Rep, 34, 11-17.  
16912867 P.M.McNutt, M.J.Dehart, and L.A.Matej (2007).
Characterization of the 16S-23S internal transcribed spacer among 34 higher plants: suitability for interspecific plastid transformation.
  Plant Cell Rep, 26, 47-60.  
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
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.  
17921318 S.Chaudhuri, K.Vyas, P.Kapasi, A.A.Komar, J.D.Dinman, S.Barik, and B.Mazumder (2007).
Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation.
  RNA, 13, 2224-2237.  
17942742 S.J.Näsvall, P.Chen, and G.R.Björk (2007).
The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.
  RNA, 13, 2151-2164.  
17766247 S.N.Hobbie, S.K.Kalapala, S.Akshay, C.Bruell, S.Schmidt, S.Dabow, A.Vasella, P.Sander, and E.C.Böttger (2007).
Engineering the rRNA decoding site of eukaryotic cytosolic ribosomes in bacteria.
  Nucleic Acids Res, 35, 6086-6093.  
17539821 S.O.Meroueh, and S.Mobashery (2007).
Conformational transition in the aminoacyl t-RNA site of the bacterial ribosome both in the presence and absence of an aminoglycoside antibiotic.
  Chem Biol Drug Des, 69, 291-297.  
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.  
17218280 U.Kothe, and M.V.Rodnina (2007).
Codon reading by tRNAAla with modified uridine in the wobble position.
  Mol Cell, 25, 167-174.  
17319662 V.K.Tam, D.Kwong, and Y.Tor (2007).
Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery.
  J Am Chem Soc, 129, 3257-3266.  
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
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.  
16510876 A.V.Pisarev, V.G.Kolupaeva, V.P.Pisareva, W.C.Merrick, C.U.Hellen, and T.V.Pestova (2006).
Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex.
  Genes Dev, 20, 624-636.  
17188032 C.Hoang, J.Chen, C.A.Vizthum, J.M.Kandel, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2006).
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
  Mol Cell, 24, 535-545.
PDB code: 2i82
17381338 E.M.Youngman, L.Cochella, J.L.Brunelle, S.He, and R.Green (2006).
Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors.
  Cold Spring Harb Symp Quant Biol, 71, 545-549.  
17188037 F.J.LaRiviere, S.E.Cole, D.J.Ferullo, and M.J.Moore (2006).
A late-acting quality control process for mature eukaryotic rRNAs.
  Mol Cell, 24, 619-626.  
16891415 F.S.Liang, W.A.Greenberg, J.A.Hammond, J.Hoffmann, S.R.Head, and C.H.Wong (2006).
Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays.
  Proc Natl Acad Sci U S A, 103, 12311-12316.  
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
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.  
16371706 G.Rosenbaum, R.W.Alkire, G.Evans, F.J.Rotella, K.Lazarski, R.G.Zhang, S.L.Ginell, N.Duke, I.Naday, J.Lazarz, M.J.Molitsky, L.Keefe, J.Gonczy, L.Rock, R.Sanishvili, M.A.Walsh, E.Westbrook, and A.Joachimiak (2006).
The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
  J Synchrotron Radiat, 13, 30-45.  
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
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.  
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.  
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
16596680 J.Kondo, B.François, A.Urzhumtsev, and E.Westhof (2006).
Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin.
  Angew Chem Int Ed Engl, 45, 3310-3314.
PDB code: 2g5k
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.  
16455492 K.B.Gromadski, T.Daviter, and M.V.Rodnina (2006).
A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity.
  Mol Cell, 21, 369-377.  
16890441 K.P.Hofmann, C.M.Spahn, R.Heinrich, and U.Heinemann (2006).
Building functional modules from molecular interactions.
  Trends Biochem Sci, 31, 497-508.  
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.  
16699167 L.Brandi, A.Fabbretti, M.Di Stefano, A.Lazzarini, M.Abbondi, and C.O.Gualerzi (2006).
Characterization of GE82832, a peptide inhibitor of translocation interacting with bacterial 30S ribosomal subunits.
  RNA, 12, 1262-1270.  
17012271 N.E.McCrate, M.E.Varner, K.I.Kim, and M.C.Nagan (2006).
Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.
  Nucleic Acids Res, 34, 5361-5368.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
16510980 R.Utsunomiya, K.Suto, D.Balasundaresan, A.Fukamizu, P.K.Kumar, and H.Mizuno (2006).
Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.
  Acta Crystallogr D Biol Crystallogr, 62, 331-338.
PDB code: 2ao5
16406634 S.P.Yates, R.Jørgensen, G.R.Andersen, and A.R.Merrill (2006).
Stealth and mimicry by deadly bacterial toxins.
  Trends Biochem Sci, 31, 123-133.  
16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.
  Mol Microbiol, 59, 1664-1677.  
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
16214802 B.François, R.J.Russell, J.B.Murray, F.Aboul-ela, B.Masquida, Q.Vicens, and E.Westhof (2005).
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.
  Nucleic Acids Res, 33, 5677-5690.
PDB codes: 2esi 2esj 2et3 2et4 2et5 2et8
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.  
15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
  FEBS J, 272, 2098-2108.  
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
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15872184 F.Bélanger, G.Théberge-Julien, P.R.Cunningham, and L.Brakier-Gingras (2005).
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16111914 J.A.Sutcliffe (2005).
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15980485 J.Kleinjung, and F.Fraternali (2005).
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15952884 J.M.Ogle, and V.Ramakrishnan (2005).
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16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
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15905403 L.Cochella, and R.Green (2005).
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16061180 L.R.Cruz-Vera, S.Rajagopal, C.Squires, and C.Yanofsky (2005).
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16228651 M.A.Line (2005).
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15840820 M.Guillier, F.Allemand, M.Graffe, S.Raibaud, F.Dardel, M.Springer, and C.Chiaruttini (2005).
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16177134 M.Kwapisz, P.Cholbinski, A.K.Hopper, J.P.Rousset, and T.Zoladek (2005).
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16244134 M.N.Lambert, J.A.Hoerter, M.J.Pereira, and N.G.Walter (2005).
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16116437 M.Olejniczak, T.Dale, R.P.Fahlman, and O.C.Uhlenbeck (2005).
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16004388 N.A.Demeshkina, V.A.Stiazhkina, K.N.Bulygin, M.N.Repkova, A.G.Ven'iaminova, and G.G.Karpova (2005).
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16177132 N.M.Abdi, and K.Fredrick (2005).
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15849690 Q.Han, Q.Zhao, S.Fish, K.B.Simonsen, D.Vourloumis, J.M.Froelich, D.Wall, and T.Hermann (2005).
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PDB code: 1yrj
16107839 R.Jørgensen, A.R.Merrill, S.P.Yates, V.E.Marquez, A.L.Schwan, T.Boesen, and G.R.Andersen (2005).
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PDB codes: 1zm2 1zm3 1zm4 1zm9
16043501 S.Q.Gu, J.Jöckel, P.Beinker, J.Warnecke, Y.P.Semenkov, M.V.Rodnina, and W.Wintermeyer (2005).
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15699355 T.R.Sundermeier, D.P.Dulebohn, H.J.Cho, and A.W.Karzai (2005).
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14681588 A.L.Konevega, N.G.Soboleva, V.I.Makhno, Y.P.Semenkov, W.Wintermeyer, M.V.Rodnina, and V.I.Katunin (2004).
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15593140 B.François, J.Szychowski, S.S.Adhikari, K.Pachamuthu, E.E.Swayze, R.H.Griffey, M.T.Migawa, E.Westhof, and S.Hanessian (2004).
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PDB codes: 2be0 2bee
15208366 D.Graifer, M.Molotkov, V.Styazhkina, N.Demeshkina, K.Bulygin, A.Eremina, A.Ivanov, E.Laletina, A.Ven'yaminova, and G.Karpova (2004).
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15523473 D.N.Wilson, and K.H.Nierhaus (2004).
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14681582 D.Rodriguez-Correa, and A.E.Dahlberg (2004).
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PDB codes: 1xnq 1xnr
15558052 F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, and P.F.Agris (2004).
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PDB codes: 1xmo 1xmq
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15509870 M.O'Connor, S.T.Gregory, and A.E.Dahlberg (2004).
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15574334 R.P.Fahlman, T.Dale, and O.C.Uhlenbeck (2004).
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15112238 W.P.Tate, and E.S.Poole (2004).
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12820965 A.Savelsbergh, V.I.Katunin, D.Mohr, F.Peske, M.V.Rodnina, and W.Wintermeyer (2003).
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12592009 C.C.Correll, and K.Swinger (2003).
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.
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PDB code: 1msy
12907716 C.M.Duarte, L.M.Wadley, and A.M.Pyle (2003).
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
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12598368 D.L.Theobald, R.M.Mitton-Fry, and D.S.Wuttke (2003).
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12932345 D.R.Southworth, and R.Green (2003).
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Novel acyclic deoxystreptamine mimetics targeting the ribosomal decoding site.
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12554858 E.P.Plant, K.L.Jacobs, J.W.Harger, A.Meskauskas, J.L.Jacobs, J.L.Baxter, A.N.Petrov, and J.D.Dinman (2003).
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
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12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
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Translational selection and yeast proteome evolution.
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12809609 H.Gao, J.Sengupta, M.Valle, A.Korostelev, N.Eswar, S.M.Stagg, P.Van Roey, R.K.Agrawal, S.C.Harvey, A.Sali, M.S.Chapman, and J.Frank (2003).
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PDB codes: 1p6g 1p85 1p86 1p87
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Toward an understanding of the structural basis of translation.
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Electron microscopy of functional ribosome complexes.
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12964164 K.B.Simonsen, B.K.Ayida, D.Vourloumis, G.C.Winters, M.Takahashi, S.Shandrick, Q.Zhao, and T.Hermann (2003).
Piperidine glycosides targeting the ribosomal decoding site.
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PDB codes: 1qza 1qzb 1qzc 1qzd 1r2w 1r2x
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Analysis of RNA motifs.
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14527328 P.B.Moore, and T.A.Steitz (2003).
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12925992 Q.Vicens, and E.Westhof (2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
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14523919 Q.Vicens, and E.Westhof (2003).
RNA as a drug target: the case of aminoglycosides.
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12857776 S.B.Vakulenko, and S.Mobashery (2003).
Versatility of aminoglycosides and prospects for their future.
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Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking.
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After the ribosome structure: how does translocation work?
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12517339 S.R.Lynch, R.L.Gonzalez, and J.D.Puglisi (2003).
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12932729 T.A.Steitz, and P.B.Moore (2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
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12717454 T.M.Hansen, P.V.Baranov, I.P.Ivanov, R.F.Gesteland, and J.F.Atkins (2003).
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14561884 T.M.Schmeing, P.B.Moore, and T.A.Steitz (2003).
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PDB codes: 1qvf 1qvg
12711689 T.Nishiyama, H.Yamamoto, N.Shibuya, Y.Hatakeyama, A.Hachimori, T.Uchiumi, and N.Nakashima (2003).
Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes.
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12839808 Y.Okamoto-Hosoya, S.Okamoto, and K.Ochi (2003).
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Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer.
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12244299 A.Kuglstatter, C.Oubridge, and K.Nagai (2002).
Induced structural changes of 7SL RNA during the assembly of human signal recognition particle.
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The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
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12189204 D.J.Battle, and J.A.Doudna (2002).
Specificity of RNA-RNA helix recognition.
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Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
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11927566 E.Schmitt, S.Blanquet, and Y.Mechulam (2002).
The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
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PDB codes: 1kjz 1kk0 1kk1 1kk2 1kk3
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tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.
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Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation.
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12034847 G.Caetano-Anollés (2002).
Tracing the evolution of RNA structure in ribosomes.
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11943544 G.Stahl, G.P.McCarty, and P.J.Farabaugh (2002).
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Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
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PDB code: 1mj1
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The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
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12270832 J.Ma, A.Campbell, and S.Karlin (2002).
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Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA.
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11911360 L.Frolova, A.Seit-Nebi, and L.Kisselev (2002).
Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1.
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11959595 R.Mehta, and W.S.Champney (2002).
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The tetracycline resistance protein Tet(o) perturbs the conformation of the ribosomal decoding centre.
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12419224 S.S.Phelps, O.Jerinic, and S.Joseph (2002).
Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation.
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11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
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rRNA modifications and ribosome function.
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Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome.
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11701127 C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, and J.Frank (2001).
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PDB codes: 1k5x 1k5y
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12762016 G.Blaha, and K.H.Nierhaus (2001).
Features and functions of the ribosomal E site.
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11566123 G.M.Culver (2001).
Meanderings of the mRNA through the ribosome.
  Structure, 9, 751-758.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
12762026 G.Stahl, S.Ben Salem, Z.Li, G.McCarty, A.Raman, M.Shah, and P.J.Farabaugh (2001).
Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction.
  Cold Spring Harb Symp Quant Biol, 66, 249-258.  
11511350 G.Z.Yusupova, M.M.Yusupov, J.H.Cate, and H.F.Noller (2001).
The path of messenger RNA through the ribosome.
  Cell, 106, 233-241.
PDB codes: 1jgo 1jgp 1jgq
12762008 H.F.Noller, M.M.Yusupov, G.Z.Yusupova, A.Baucom, K.Lieberman, L.Lancaster, A.Dallas, K.Fredrick, T.N.Earnest, and J.H.Cate (2001).
Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
  Cold Spring Harb Symp Quant Biol, 66, 57-66.  
12762017 J.Ofengand, A.Malhotra, J.Remme, N.S.Gutgsell, M.Del Campo, S.Jean-Charles, L.Peil, and Y.Kaya (2001).
Pseudouridines and pseudouridine synthases of the ribosome.
  Cold Spring Harb Symp Quant Biol, 66, 147-159.  
11517305 M.A.Bayfield, A.E.Dahlberg, U.Schulmeister, S.Dorner, and A.Barta (2001).
A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition.
  Proc Natl Acad Sci U S A, 98, 10096-10101.  
12762059 S.A.Gerbi, A.V.Borovjagin, M.Ezrokhi, and T.S.Lange (2001).
Ribosome biogenesis: role of small nucleolar RNA in maturation of eukaryotic rRNA.
  Cold Spring Harb Symp Quant Biol, 66, 575-590.  
11532943 T.Yasukawa, T.Suzuki, N.Ishii, S.Ohta, and K.Watanabe (2001).
Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease.
  EMBO J, 20, 4794-4802.  
11453067 V.I.Lim, and J.F.Curran (2001).
Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure.
  RNA, 7, 942-957.  
11714910 W.Li, and D.W.Hoffman (2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
  Protein Sci, 10, 2426-2438.
PDB code: 1jt8
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.