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PDBsum entry 1ml5

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protein dna_rna links
Ribosome PDB id
1ml5
Jmol PyMol
Contents
Protein chains
362 a.a.* *
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.* *
224 a.a.* *
173 a.a.* *
191 a.a.* *
189 a.a.* *
122 a.a.* *
164 a.a.* *
133 a.a.* *
117 a.a.* *
122 a.a.* *
84 a.a.* *
138 a.a.* *
113 a.a.* *
52 a.a.* *
110 a.a.* *
76 a.a.* *
110 a.a.* *
89 a.a.* *
64 a.a.* *
60 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1ml5
Name: Ribosome
Title: Structure of the e. Coli ribosomal termination complex with factor 2
Structure: 30s 16s ribosomal RNA. Chain: a. T-RNA(phe). Chain: b. Other_details: tRNA p-site. A- and p-site messenger RNA codons. Chain: c. Other_details: 6 nt long mRNA fragment. 50s 23s ribosomal RNA.
Source: Escherichia coli. Organism_taxid: 562. Gene: prfb/supk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Organism_taxid: 562
Authors: B.P.Klaholz,T.Pape,A.V.Zavialov,A.G.Myasnikov,E.V.Orlova, B.Vestergaard,M.Ehrenberg,M.Van Heel
Key ref:
B.P.Klaholz et al. (2003). Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature, 421, 90-94. PubMed id: 12511961 DOI: 10.1038/nature01225
Date:
30-Aug-02     Release date:   14-Jan-03    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07012  (RF2_ECOLI) -  Peptide chain release factor RF2
Seq:
Struc:
365 a.a.
362 a.a.
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 ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam  
A0A0M9AFS9  (RS8_THEAQ) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 a.a.
Protein chain
Pfam  
A0A0N0BLP2  (RS14Z_THEAQ) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
83 a.a.
Protein chain
Pfam  
A0A0N0BLS5  (RS17_THEAQ) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
24 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP7  (RL1_THET8) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
224 a.a.*
Protein chain
Pfam   ArchSchema ?
P04257  (RL2_GEOSE) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
173 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  50S ribosomal protein L3
Seq:
Struc:
338 a.a.
191 a.a.*
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  50S ribosomal protein L4
Seq:
Struc:
246 a.a.
189 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  50S ribosomal protein L5
Seq:
Struc:
177 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5L408  (RL6_GEOKA) -  50S ribosomal protein L6
Seq:
Struc:
178 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc:
141 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  50S ribosomal protein L13
Seq:
Struc:
145 a.a.
117 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5L413  (RL14_GEOKA) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  50S ribosomal protein L15
Seq:
Struc:
165 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P60617  (RL10_HALMA) -  50S ribosomal protein L10e
Seq:
Struc:
177 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  50S ribosomal protein L18
Seq:
Struc:
187 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  50S ribosomal protein L24e
Seq:
Struc:
67 a.a.
52 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  50S ribosomal protein L23
Seq:
Struc:
85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  50S ribosomal protein L24
Seq:
Struc:
120 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
89 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  50S ribosomal protein L29
Seq:
Struc:
71 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
60 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 126 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   8 terms 
  Biological process     regulation of translation   5 terms 
  Biochemical function     structural constituent of ribosome     10 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature01225 Nature 421:90-94 (2003)
PubMed id: 12511961  
 
 
Structure of the Escherichia coli ribosomal termination complex with release factor 2.
B.P.Klaholz, T.Pape, A.V.Zavialov, A.G.Myasnikov, E.V.Orlova, B.Vestergaard, M.Ehrenberg, M.van Heel.
 
  ABSTRACT  
 
Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Detailed stereo views of RF2 -ribosome interactions at the level of the decoding site and the PTC. Domain 1 of RF2 is shown in red, domain 2/4 in orange, and domain 3 in yellow. Ribosomal RNAs are coloured in blue, proteins in green, and mRNA and the P-site tRNA in magenta. a, Decoding centre: domains 2 and 4 form a unit embedded between helix 18 of 16S RNA and protein S12 on one side, and helices 44 of 16S RNA and 69 of 23S RNA on the other. The tip of domain 2 containing the SPF-motif loop can reach the stop codon. b, PTC: domain 3 extends from helix 69 of 23S RNA towards the PTC, contacting helices 71, 89 and 92 of 23S RNA, and P-site tRNA. The flexible GGQ loop is close to helix 93 and to the P-site tRNA 3' end.
Figure 3.
Figure 3: The derived in situ RF2 structure and its interaction pattern. The RF2 domains are colour-coded as in Fig. 2. The two functional important sites for decoding (SPF loop) and peptide hydrolysis (GGQ loop) are indicated. a, In situ RF2 areas involved in transmission of the decoding signal (left) to the PTC (bottom right). The main ribosomal proteins and RNA helices involved are indicated. b, Superposition of in situ RF2 with the RF2 crystal structure (PDB code 1GQE, shown in blue)6 using domain 2/4 as an anchor. The conformational change occurring on binding to the ribosome apparently allows RF2 to contact both ribosomal active sites directly. c, Superposition with the eRF1 crystal structure (PDB code 1DT9 (ref. 5), shown in purple) using domain 2/4 of RF2 and the decoding domain 1 of eRF1 as an anchor. Domain 2 of eRF1 is proposed to undergo a rearrangement on binding to the ribosome so that the universally conserved GGQ motifs in this diagram will be in similar positions. d, Superposition with A-site tRNA (PDB code 1GIY (ref. 10), shown in green) in its position in the 70S ribosome crystal structure. RF2 seems to mimic a tRNA in functional terms but less so in structural terms. Stereo representations may be viewed in Supplementary Information.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 421, 90-94) copyright 2003.  
  Figures were selected by an automated process.  

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.  
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
  Biochimie, 93, 834-844.  
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
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
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.  
20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
  J Struct Biol, 170, 164-171.  
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
19820108 A.Baudin-Baillieu, C.Fabret, X.H.Liang, D.Piekna-Przybylska, M.J.Fournier, and J.P.Rousset (2009).
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy.
  Nucleic Acids Res, 37, 7665-7677.  
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.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
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.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
18758445 A.Simonetti, S.Marzi, A.G.Myasnikov, A.Fabbretti, M.Yusupov, C.O.Gualerzi, and B.P.Klaholz (2008).
Structure of the 30S translation initiation complex.
  Nature, 455, 416-420.  
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
18347330 D.F.Kelly, D.Dukovski, and T.Walz (2008).
Monolayer purification: a rapid method for isolating protein complexes for single-particle electron microscopy.
  Proc Natl Acad Sci U S A, 105, 4703-4708.  
18655791 D.F.Kelly, P.D.Abeyrathne, D.Dukovski, and T.Walz (2008).
The Affinity Grid: a pre-fabricated EM grid for monolayer purification.
  J Mol Biol, 382, 423-433.  
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
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
18805973 T.Monshupanee, S.T.Gregory, S.Douthwaite, W.Chungjatupornchai, and A.E.Dahlberg (2008).
Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications.
  J Bacteriol, 190, 7754-7761.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
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.  
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.  
  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.  
17889647 S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, and B.P.Klaholz (2007).
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
  Cell, 130, 1019-1031.
PDB code: 2vaz
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.  
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.  
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.  
16284619 A.G.Myasnikov, S.Marzi, A.Simonetti, A.M.Giuliodori, C.O.Gualerzi, G.Yusupova, M.Yusupov, and B.P.Klaholz (2005).
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.
  Nat Struct Mol Biol, 12, 1145-1149.  
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.  
16043503 H.Liang, and L.F.Landweber (2005).
Molecular mimicry: quantitative methods to study structural similarity between protein and RNA.
  RNA, 11, 1167-1172.  
16199759 H.Liang, L.F.Landweber, and J.R.Fresco (2005).
Are stop codons recognized by base triplets in the large ribosomal RNA subunit?
  RNA, 11, 1478-1484.  
16061180 L.R.Cruz-Vera, S.Rajagopal, C.Squires, and C.Yanofsky (2005).
Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression.
  Mol Cell, 19, 333-343.  
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.  
16174429 O.Llorca (2005).
Introduction to 3D reconstruction of macromolecules using single particle electron microscopy.
  Acta Pharmacol Sin, 26, 1153-1164.  
16094695 S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, and J.Wöhnert (2005).
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
  Chembiochem, 6, 1611-1618.
PDB code: 2k3f
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
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.  
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.  
14734569 J.Towpik, A.Chaciñska, M.Ciesla, K.Ginalski, and M.Boguta (2004).
Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes.
  J Biol Chem, 279, 14096-14103.  
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.  
15112238 W.P.Tate, and E.S.Poole (2004).
The ribosome: lifting the veil from a fascinating organelle.
  Bioessays, 26, 582-588.  
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.  
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
12589713 S.E.Moskalenko, S.V.Chabelskaya, S.G.Inge-Vechtomov, M.Philippe, and G.A.Zhouravleva (2003).
Viable nonsense mutants for the essential gene SUP45 of Saccharomyces cerevisiae.
  BMC Mol Biol, 4, 2.  
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 code is shown on the right.

 

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