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protein dna_rna links
Ribosome PDB id
1mvr
Jmol
Contents
Protein chains
124 a.a.* *
133 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1mvr
Name: Ribosome
Title: Decoding center & peptidyl transferase center from the x-ray of the thermus thermophilus 70s ribosome, aligned to the lo resolution cryo-em map of e.Coli 70s ribosome
Structure: mRNA, triplet codon (a-site). Chain: 1. Other_details: based on coordinates from 1gix, 30s subunit. Helix 34 of 16s rrna. Chain: a. Other_details: based on coordinates from 1gix, 30s subunit. Helix 44 of 16s rrna. Chain: b. Other_details: based on coordinates from 1gix, 30s subunit.
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Strain: k12
Authors: U.B.Rawat,A.V.Zavialov,J.Sengupta,M.Valle,R.A.Grassucci,J.Li B.Vestergaard,M.Ehrenberg,J.Frank
Key ref:
U.B.Rawat et al. (2003). A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature, 421, 87-90. PubMed id: 12511960 DOI: 10.1038/nature01224
Date:
26-Sep-02     Release date:   01-Apr-03    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc: 		132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc: 		141 a.a.
133 a.a.
Key:    PfamA domain  Secondary structure

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

 

 
    Added reference    
 
 
DOI no: 10.1038/nature01224 Nature 421:87-90 (2003)
PubMed id: 12511960  
 
 
A cryo-electron microscopic study of ribosome-bound termination factor RF2.
U.B.Rawat, A.V.Zavialov, J.Sengupta, M.Valle, R.A.Grassucci, J.Linde, B.Vestergaard, M.Ehrenberg, J.Frank.
 
  ABSTRACT  
 
Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Interaction of RC with RF2. Three-dimensional maps of the RC with RF2(GAQ) mutant (a) and RF2(wt) (b). Yellow, 30S subunit; blue, 50S subunit. c, d, Fitting of modified X-ray structure of RF2 into cryo-density of RF2(GAQ) (c) and RF2(wt) (d). Ribosome features: sh, shoulder; sp, spur; St, L7/L12 stalk; P, P-site tRNA; DC, decoding centre; PTC, peptidyl-transferase centre; GAC, GTPase-associated centre. Colour coding for RF2: orange, RF2(GAQ); magenta, RF2(wt); gold, domain I; purple, domain II; red, domain III; green, domain IV; magenta, SPF; grey, GGQ. Flexible regions between RF2 domains: cyan, I -II; pale red, II -III; pale green, III -IV. Asterisks in c and d mark conformational changes in domain III. Density to the right of the dotted line in c is due to a conformational change of the ribosome. 		Figure 2.
Figure 2: CPK (Corey -Pauling -Koltun) representation of RF2 domain constellations in the two conformations. a, b, X-ray structure; c, d, cryo-EM structure. The X-ray and cryo-EM structures of RF2 are shown in orientations such that domain I is aligned in each. Colour coding for RF2: gold, domain I; purple, domain II; red, domain III; green, domain IV; magenta, SPF; grey, GGQ. Flexible region between RF2 domains: cyan, I -II; pale red, II -III; pale green, III -IV.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 421, 87-90) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
21428957 M.V.Rodnina, and W.Wintermeyer (2011).
The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation.
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21051357 Y.Handa, N.Inaho, and N.Nameki (2011).
YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes.
  Nucleic Acids Res, 39, 1739-1748.  
20588254 A.Korostelev, J.Zhu, H.Asahara, and H.F.Noller (2010).
Recognition of the amber UAG stop codon by release factor RF1.
  EMBO J, 29, 2577-2585.
PDB codes: 3mr8 3mrz 3ms0 3ms1
  20634984 C.Gorba, and F.Tama (2010).
Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.
  Bioinform Biol Insights, 4, 43-54.  
20421507 H.Jin, A.C.Kelley, D.Loakes, and V.Ramakrishnan (2010).
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
  Proc Natl Acad Sci U S A, 107, 8593-8598.
PDB codes: 2x9r 2x9s 2x9t 2x9u
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20512119 J.Sund, M.Andér, and J.Aqvist (2010).
Principles of stop-codon reading on the ribosome.
  Nature, 465, 947-950.  
20085819 M.Shatsky, R.J.Hall, E.Nogales, J.Malik, and S.E.Brenner (2010).
Automated multi-model reconstruction from single-particle electron microscopy data.
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20729861 T.Yanagisawa, T.Sumida, R.Ishii, C.Takemoto, and S.Yokoyama (2010).
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
  Nat Struct Mol Biol, 17, 1136-1143.
PDB codes: 3a5y 3a5z
20004164 A.Matsumoto, and H.Ishida (2009).
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures.
  Structure, 17, 1605-1613.  
19874047 B.Hetrick, K.Lee, and S.Joseph (2009).
Kinetics of stop codon recognition by release factor 1.
  Biochemistry, 48, 11178-11184.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
  19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
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19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
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
17680691 A.V.Kononenko, V.A.Mitkevich, V.I.Dubovaya, P.M.Kolosov, A.A.Makarov, and L.L.Kisselev (2008).
Role of the individual domains of translation termination factor eRF1 in GTP binding to eRF3.
  Proteins, 70, 388-393.  
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
17993489 C.Gorba, O.Miyashita, and F.Tama (2008).
Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data.
  Biophys J, 94, 1589-1599.  
18544041 E.M.Youngman, M.E.McDonald, and R.Green (2008).
Peptide release on the ribosome: mechanism and implications for translational control.
  Annu Rev Microbiol, 62, 353-373.  
18224323 J.Kutner, J.Towpik, K.Ginalski, and M.Boguta (2008).
Mitochondrial release factor in yeast: interplay of functional domains.
  Curr Genet, 53, 185-192.  
18369182 M.Beringer (2008).
Modulating the activity of the peptidyl transferase center of the ribosome.
  RNA, 14, 795-801.  
18596689 M.Laurberg, H.Asahara, A.Korostelev, J.Zhu, S.Trakhanov, and H.F.Noller (2008).
Structural basis for translation termination on the 70S ribosome.
  Nature, 454, 852-857.
PDB codes: 3d5a 3d5b 3d5c 3d5d
18849406 M.Orzechowski, and F.Tama (2008).
Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.
  Biophys J, 95, 5692-5705.  
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
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
18619547 T.R.Shaikh, R.Trujillo, J.S.LeBarron, W.T.Baxter, and J.Frank (2008).
Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification.
  J Struct Biol, 164, 41-48.  
18094470 Y.Xiong (2008).
From electron microscopy to X-ray crystallography: molecular-replacement case studies.
  Acta Crystallogr D Biol Crystallogr, 64, 76-82.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
17292917 D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, and Y.X.Wang (2007).
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
  J Mol Biol, 367, 1007-1022.
PDB codes: 2e34 2e35 2e36 2h8w
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.  
17621307 E.S.Poole, D.J.Young, M.E.Askarian-Amiri, D.J.Scarlett, and W.P.Tate (2007).
Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome.
  Cell Res, 17, 591-607.  
17651434 E.V.Ivanova, P.M.Kolosov, B.Birdsall, G.Kelly, A.Pastore, L.L.Kisselev, and V.I.Polshakov (2007).
Eukaryotic class 1 translation termination factor eRF1--the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis.
  FEBS J, 274, 4223-4237.
PDB code: 2hst
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
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.  
17996709 J.J.Shaw, and R.Green (2007).
Two distinct components of release factor function uncovered by nucleophile partitioning analysis.
  Mol Cell, 28, 458-467.  
18056798 K.Mossman, and J.Frank (2007).
Profile of Joachim Frank.
  Proc Natl Acad Sci U S A, 104, 19668-19670.  
17660192 M.Amort, B.Wotzel, K.Bakowska-Zywicka, M.D.Erlacher, R.Micura, and N.Polacek (2007).
An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination.
  Nucleic Acids Res, 35, 5130-5140.  
18032607 M.Ejby, M.A.Sørensen, and S.Pedersen (2007).
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination.
  Proc Natl Acad Sci U S A, 104, 19410-19415.  
  17329807 N.Okazaki, M.Kumei, M.Manzoku, S.Kuramitsu, M.Shirouzu, A.Shinkai, and S.Yokoyama (2007).
Structure of a UPF0150-family protein from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 173-177.
PDB code: 2dsy
17573528 S.Lekomtsev, P.Kolosov, L.Bidou, L.Frolova, J.P.Rousset, and L.Kisselev (2007).
Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors.
  Proc Natl Acad Sci U S A, 104, 10824-10829.  
16614446 A.G.Cridge, L.L.Major, A.A.Mahagaonkar, E.S.Poole, L.A.Isaksson, and W.P.Tate (2006).
Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms.
  Nucleic Acids Res, 34, 1959-1973.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16943448 F.Tama, G.Ren, C.L.Brooks, and A.K.Mitra (2006).
Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer.
  Protein Sci, 15, 2190-2200.  
16556224 H.Sato, K.Ito, and Y.Nakamura (2006).
Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity.
  Mol Microbiol, 60, 108-120.  
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.  
16476727 K.Higashi, K.Kashiwagi, S.Taniguchi, Y.Terui, K.Yamamoto, A.Ishihama, and K.Igarashi (2006).
Enhancement of +1 frameshift by polyamines during translation of polypeptide release factor 2 in Escherichia coli.
  J Biol Chem, 281, 9527-9537.  
16371360 L.Bouakaz, E.Bouakaz, E.J.Murgola, M.Ehrenberg, and S.Sanyal (2006).
The role of ribosomal protein L11 in class I release factor-mediated translation termination and translational accuracy.
  J Biol Chem, 281, 4548-4556.  
16621804 N.Hirabayashi, N.S.Sato, and T.Suzuki (2006).
Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity.
  J Biol Chem, 281, 17203-17211.  
16970810 P.V.Baranov, B.Vestergaard, T.Hamelryck, R.F.Gesteland, J.Nyborg, and J.F.Atkins (2006).
Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons.
  Biol Direct, 1, 28.  
17062564 V.P.Pisareva, A.V.Pisarev, C.U.Hellen, M.V.Rodnina, and T.V.Pestova (2006).
Kinetic analysis of interaction of eukaryotic release factor 3 with guanine nucleotides.
  J Biol Chem, 281, 40224-40235.  
16053518 A.Liiv, D.Karitkina, U.Maiväli, and J.Remme (2005).
Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis.
  BMC Mol Biol, 6, 18.  
15985150 A.V.Zavialov, V.V.Hauryliuk, and M.Ehrenberg (2005).
Guanine-nucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs.
  J Biol, 4, 9.  
16272117 B.S.Schuwirth, M.A.Borovinskaya, C.W.Hau, W.Zhang, A.Vila-Sanjurjo, J.M.Holton, and J.H.Cate (2005).
Structures of the bacterial ribosome at 3.5 A resolution.
  Science, 310, 827-834.
PDB codes: 2avy 2aw4 2aw7 2awb
16364917 B.Vestergaard, S.Sanyal, M.Roessle, L.Mora, R.H.Buckingham, J.S.Kastrup, M.Gajhede, D.I.Svergun, and M.Ehrenberg (2005).
The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure.
  Mol Cell, 20, 929-938.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16043503 H.Liang, and L.F.Landweber (2005).
Molecular mimicry: quantitative methods to study structural similarity between protein and RNA.
  RNA, 11, 1167-1172.  
15897324 M.A.Xaplanteri, A.D.Petropoulos, G.P.Dinos, and D.L.Kalpaxis (2005).
Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions.
  Nucleic Acids Res, 33, 2792-2805.  
15989950 M.Diaconu, U.Kothe, F.Schlünzen, N.Fischer, J.M.Harms, A.G.Tonevitsky, H.Stark, M.V.Rodnina, and M.C.Wahl (2005).
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation.
  Cell, 121, 991.
PDB codes: 1zav 1zaw 1zax 1zb4
16364916 M.Graille, V.Heurgué-Hamard, S.Champ, L.Mora, N.Scrima, N.Ulryck, H.van Tilbeurgh, and R.H.Buckingham (2005).
Molecular basis for bacterial class I release factor methylation by PrmC.
  Mol Cell, 20, 917-927.
PDB code: 2b3t
16162810 N.J.Oparina, O.V.Kalinina, M.S.Gelfand, and L.L.Kisselev (2005).
Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications.
  Nucleic Acids Res, 33, 5226-5234.  
16257828 N.Polacek, and A.S.Mankin (2005).
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.
  Crit Rev Biochem Mol Biol, 40, 285-311.  
16174429 O.Llorca (2005).
Introduction to 3D reconstruction of macromolecules using single particle electron microscopy.
  Acta Pharmacol Sin, 26, 1153-1164.  
15972821 S.L.Bausch, E.Poliakova, and D.E.Draper (2005).
Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA.
  J Biol Chem, 280, 29956-29963.  
16377566 S.Petry, D.E.Brodersen, F.V.Murphy, C.M.Dunham, M.Selmer, M.J.Tarry, A.C.Kelley, and V.Ramakrishnan (2005).
Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.
  Cell, 123, 1255-1266.
PDB codes: 2b64 2b66 2b9m 2b9n 2b9o 2b9p
16306996 T.M.Schmeing, K.S.Huang, S.A.Strobel, and T.A.Steitz (2005).
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
  Nature, 438, 520-524.
PDB codes: 1vq6 1vq7 1vqn
15612924 T.Yamami, K.Ito, T.Fujiwara, and Y.Nakamura (2005).
Heterologous expression of Aquifex aeolicus ribosome recycling factor in Escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly.
  Mol Microbiol, 55, 150-161.  
15509572 V.Heurgué-Hamard, S.Champ, L.Mora, T.Merkulova-Rainon, T.Merkoulova-Rainon, L.L.Kisselev, and R.H.Buckingham (2005).
The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene.
  J Biol Chem, 280, 2439-2445.  
15475364 B.Ma, and R.Nussinov (2004).
Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes.
  J Biol Chem, 279, 53875-53885.  
14985767 B.P.Klaholz, A.G.Myasnikov, and M.Van Heel (2004).
Visualization of release factor 3 on the ribosome during termination of protein synthesis.
  Nature, 427, 862-865.  
14976550 C.M.Spahn, M.G.Gomez-Lorenzo, R.A.Grassucci, R.Jørgensen, G.R.Andersen, R.Beckmann, P.A.Penczek, J.P.Ballesta, and J.Frank (2004).
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
  EMBO J, 23, 1008-1019.
PDB codes: 1s1h 1s1i
15163407 E.M.Youngman, J.L.Brunelle, A.B.Kochaniak, and R.Green (2004).
The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release.
  Cell, 117, 589-599.  
15465319 E.V.Orlova, and H.R.Saibil (2004).
Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs.
  Curr Opin Struct Biol, 14, 584-590.  
15561874 J.Thompson, C.A.Pratt, and A.E.Dahlberg (2004).
Effects of a number of classes of 50S inhibitors on stop codon readthrough during protein synthesis.
  Antimicrob Agents Chemother, 48, 4889-4891.  
15210970 K.Hanawa-Suetsugu, S.Sekine, H.Sakai, C.Hori-Takemoto, T.Terada, S.Unzai, J.R.Tame, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2004).
Crystal structure of elongation factor P from Thermus thermophilus HB8.
  Proc Natl Acad Sci U S A, 101, 9595-9600.
PDB code: 1ueb
15189156 L.D.Kapp, and J.R.Lorsch (2004).
The molecular mechanics of eukaryotic translation.
  Annu Rev Biochem, 73, 657-704.  
15036151 M.Gerstein, and N.Echols (2004).
Exploring the range of protein flexibility, from a structural proteomics perspective.
  Curr Opin Chem Biol, 8, 14-19.  
15178758 R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, and J.Frank (2004).
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
  Proc Natl Acad Sci U S A, 101, 8900-8905.
PDB codes: 1t1m 1t1o
15228531 T.Fujiwara, K.Ito, T.Yamami, and Y.Nakamura (2004).
Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G.
  Mol Microbiol, 53, 517-528.  
15469510 V.Vimberg, L.Xiong, M.Bailey, T.Tenson, and A.Mankin (2004).
Peptide-mediated macrolide resistance reveals possible specific interactions in the nascent peptide exit tunnel.
  Mol Microbiol, 54, 376-385.  
15112238 W.P.Tate, and E.S.Poole (2004).
The ribosome: lifting the veil from a fascinating organelle.
  Bioessays, 26, 582-588.  
15223314 Z.Yang, L.Shipman, M.Zhang, B.P.Anton, R.J.Roberts, and X.Cheng (2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
  J Mol Biol, 340, 695-706.
PDB code: 1t43
12859902 A.V.Zavialov, and M.Ehrenberg (2003).
Peptidyl-tRNA regulates the GTPase activity of translation factors.
  Cell, 114, 113-122.  
12555080 D.E.Brodersen, and V.Ramakrishnan (2003).
Shape can be seductive.
  Nat Struct Biol, 10, 78-80.  
12458201 D.J.Scarlett, K.K.McCaughan, D.N.Wilson, and W.P.Tate (2003).
Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2.
  J Biol Chem, 278, 15095-15104.  
14561879 I.S.Gabashvili, M.Whirl-Carrillo, M.Bada, D.R.Banatao, and R.B.Altman (2003).
Ribosomal dynamics inferred from variations in experimental measurements.
  RNA, 9, 1301-1307.  
12660170 L.Chavatte, S.Kervestin, A.Favre, and O.Jean-Jean (2003).
Stop codon selection in eukaryotic translation termination: comparison of the discriminating potential between human and ciliate eRF1s.
  EMBO J, 22, 1644-1653.  
14651631 L.Mora, A.Zavialov, M.Ehrenberg, and R.H.Buckingham (2003).
Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli.
  Mol Microbiol, 50, 1467-1476.  
12535516 M.Kjeldgaard (2003).
The unfolding story of polypeptide release factors.
  Mol Cell, 11, 8.  
12859903 M.Valle, A.Zavialov, J.Sengupta, U.Rawat, M.Ehrenberg, and J.Frank (2003).
Locking and unlocking of ribosomal motions.
  Cell, 114, 123-134.
PDB codes: 1pn6 1pn7 1pn8
12692531 R.Jørgensen, P.A.Ortiz, A.Carr-Schmid, P.Nissen, T.G.Kinzy, and G.R.Andersen (2003).
Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase.
  Nat Struct Biol, 10, 379-385.
PDB codes: 1n0u 1n0v
12575998 Y.Nakamura, and K.Ito (2003).
Making sense of mimic in translation termination.
  Trends Biochem Sci, 28, 99.  
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.