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PDBsum entry 2b9m
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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2b9m
Contents
Protein chains
234 a.a. *
206 a.a. *
208 a.a. *
150 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
98 a.a. *
119 a.a. *
124 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
83 a.a. *
104 a.a. *
73 a.a. *
80 a.a. *
99 a.a. *
24 a.a. *
365 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
2b9m
Name: Ribosome
Title: 30s ribosomal subunit, trnas, mRNA and release factor rf2 fr crystal structure of the whole ribosomal complex. This file the 30s ribosomal subunit, trnas, mRNA and release factor r crystal structure of the whole ribosomal complex". The enti structure contains one 70s ribosome, trnas, mRNA and releas rf2 and is described in remark 400.
Structure: 16s ribosomal RNA. Chain: a. P-site tRNA (phe). Chain: v. Engineered: yes. E-site tRNA (phe). Chain: w. Engineered: yes. 5'-d( Ap Up Gp Up Up Cp Up Ap Gp Ap Up Ap Cp Ap A
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized and gel-purified sour
Biol. unit: 25mer (from PQS)
Resolution:
6.76Å     R-factor:   0.341     R-free:   0.356
Authors: S.Petry,D.E.Brodersen,F.V.Murphy Iv,C.M.Dunham,M.Selmer,M.J. A.C.Kelley,V.Ramakrishnan
Key ref:
S.Petry et al. (2005). Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell, 123, 1255-1266. PubMed id: 16377566 DOI: 10.1016/j.cell.2005.09.039
Date:
12-Oct-05     Release date:   10-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc: 		256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
Seq:
Struc: 		239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
P27152  (RS5_THETH) -  30S ribosomal protein S5
Seq:
Struc: 		162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P23370  (RS6_THETH) -  30S ribosomal protein S6
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P24319  (RS8_THETH) -  30S ribosomal protein S8
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P62669  (RS9_THET2) -  30S ribosomal protein S9
Seq:
Struc: 		128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P80375  (RS10_THETH) -  30S ribosomal protein S10
Seq:
Struc: 		105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
No UniProt id for this chain
Struc: 124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P24320  (RS14Z_THETH) -  30S ribosomal protein S14 type Z
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P80378  (RS15_THETH) -  30S ribosomal protein S15
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc: 		88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P24321  (RS17_THETH) -  30S ribosomal protein S17
Seq:
Struc: 		105 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
P80382  (RS18_THETH) -  30S ribosomal protein S18
Seq:
Struc: 		88 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
P80381  (RS19_THETH) -  30S ribosomal protein S19
Seq:
Struc: 		93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P62661  (RS20_THET2) -  30S ribosomal protein S20
Seq:
Struc: 		106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62612  (RSHX_THETH) -  30S ribosomal protein Thx
Seq:
Struc: 		27 a.a.
24 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SM01  (Q5SM01_THET8) -  Peptide chain release factor 2
Seq:
Struc: 		378 a.a.
365 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

DNA/RNA chains
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1515 bases
  G-C-G-G-A-U-U-U-A-G-C-U-C-A-G-U-U-G-G-G-A-G-A-G-C-G-C-C-A-G-A-C-U-G-A-A-G-A-U- 76 bases
  G-C-G-G-A-U-U-U-A-G-C-U-C-A-G-U-U-G-G-G-A-G-A-G-C-G-C-C-A-G-A-C-U-G-A-A-YYG-A- 76 bases
  U-G-U-U-C-U-G-A-U-A-C-A-A-U-A-A-U 17 bases

 

 
    Key reference    
 
 
DOI no: 10.1016/j.cell.2005.09.039 Cell 123:1255-1266 (2005)
PubMed id: 16377566  
 
 
Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.
S.Petry, D.E.Brodersen, F.V.Murphy, C.M.Dunham, M.Selmer, M.J.Tarry, A.C.Kelley, V.Ramakrishnan.
 
  ABSTRACT  
 
During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Interaction of RF1 with the Decoding Center of the 30S Subunit, with Overview on the Left and Details on the Right 		Figure 6.
Figure 6. Interaction of RF1 and RF2 with the L11 Region of the Ribosome
 
  The above figures are reprinted by permission from Cell Press: Cell (2005, 123, 1255-1266) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
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.  
21804565 S.Kuhlenkoetter, W.Wintermeyer, and M.V.Rodnina (2011).
Different substrate-dependent transition states in the active site of the ribosome.
  Nature, 476, 351-354.  
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
20584893 D.J.Young, C.D.Edgar, E.S.Poole, and W.P.Tate (2010).
The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop.
  RNA, 16, 1623-1633.  
20421313 D.J.Young, C.D.Edgar, J.Murphy, J.Fredebohm, E.S.Poole, and W.P.Tate (2010).
Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria.
  RNA, 16, 1146-1155.  
20598281 H.Antonicka, E.Ostergaard, F.Sasarman, W.Weraarpachai, F.Wibrand, A.M.Pedersen, R.J.Rodenburg, M.S.van der Knaap, J.A.Smeitink, Z.M.Chrzanowska-Lightowlers, and E.A.Shoubridge (2010).
Mutations in C12orf65 in patients with encephalomyopathy and a mitochondrial translation defect.
  Am J Hum Genet, 87, 115-122.  
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.  
20676057 N.Vázquez-Laslop, H.Ramu, D.Klepacki, K.Kannan, and A.S.Mankin (2010).
The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
  EMBO J, 29, 3108-3117.  
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
19874047 B.Hetrick, K.Lee, and S.Joseph (2009).
Kinetics of stop codon recognition by release factor 1.
  Biochemistry, 48, 11178-11184.  
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.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
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
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.  
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
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.  
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
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
17998293 B.A.Maguire, L.M.Wondrack, L.G.Contillo, and Z.Xu (2008).
A novel chromatography system to isolate active ribosomes from pathogenic bacteria.
  RNA, 14, 188-195.  
18947425 G.C.Atkinson, S.L.Baldauf, and V.Hauryliuk (2008).
Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components.
  BMC Evol Biol, 8, 290.  
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.  
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.  
18332120 J.White, Z.Li, R.Sardana, J.M.Bujnicki, E.M.Marcotte, and A.W.Johnson (2008).
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.
  Mol Cell Biol, 28, 3151-3161.  
18247350 K.K.Singarapu, R.Xiao, T.Acton, B.Rost, G.T.Montelione, and T.Szyperski (2008).
NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors.
  Proteins, 71, 1027-1031.
PDB code: 2jva
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
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
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.  
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.  
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
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
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
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
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
17803939 H.R.Soleimanpour-Lichaei, I.Kühl, M.Gaisne, J.F.Passos, M.Wydro, J.Rorbach, R.Temperley, N.Bonnefoy, W.Tate, R.Lightowlers, and Z.Chrzanowska-Lightowlers (2007).
mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG.
  Mol Cell, 27, 745-757.  
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.  
18042447 J.P.Rife, and G.M.Culver (2007).
Breaking the cycle of translation.
  Mol Cell, 28, 517-519.  
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.  
17721443 L.Jenner, B.Rees, M.Yusupov, and G.Yusupova (2007).
Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography.
  EMBO Rep, 8, 846-850.  
17932046 L.Mora, V.Heurgué-Hamard, M.de Zamaroczy, S.Kervestin, and R.H.Buckingham (2007).
Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo.
  J Biol Chem, 282, 35638-35645.  
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.  
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.  
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.  
17214893 T.Margus, M.Remm, and T.Tenson (2007).
Phylogenetic distribution of translational GTPases in bacteria.
  BMC Genomics, 8, 15.  
17804412 Y.Maki, T.Hashimoto, M.Zhou, T.Naganuma, J.Ohta, T.Nomura, C.V.Robinson, and T.Uchiumi (2007).
Three binding sites for stalk protein dimers are generally present in ribosomes from archaeal organism.
  J Biol Chem, 282, 32827-32833.  
16978156 A.A.Bogdanov, V.L.Karpov, and L.L.Kisselev (2006).
RNA-protein interactions at the initial and terminal stages of protein biosynthesis as investigated by Lev Kisselev (on the occasion of his 70th anniversary).
  Biochemistry (Mosc), 71, 915-924.  
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.  
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.  
16777602 E.Z.Alkalaeva, A.V.Pisarev, L.Y.Frolova, L.L.Kisselev, and T.V.Pestova (2006).
In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3.
  Cell, 125, 1125-1136.  
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.  
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.  
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.  
16730356 S.E.Walker, and K.Fredrick (2006).
Recognition and positioning of mRNA in the ribosome by tRNAs with expanded anticodons.
  J Mol Biol, 360, 599-609.  
17008308 V.Heurgué-Hamard, M.Graille, N.Scrima, N.Ulryck, S.Champ, H.van Tilbeurgh, and R.H.Buckingham (2006).
The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast.
  J Biol Chem, 281, 36140-36148.
PDB code: 2j6a
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.  
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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