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PDBsum entry 2wh4

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2wh4
Jmol
Contents
Protein chains
76 a.a. *
94 a.a. *
71 a.a. *
60 a.a. *
30 a.a. *
59 a.a. *
45 a.a. *
49 a.a. *
64 a.a. *
36 a.a. *
191 a.a. *
272 a.a. *
205 a.a. *
208 a.a. *
181 a.a. *
160 a.a. *
146 a.a. *
130 a.a. *
141 a.a. *
139 a.a. *
122 a.a. *
146 a.a. *
141 a.a. *
117 a.a. *
99 a.a. *
138 a.a. *
117 a.a. *
101 a.a. *
113 a.a. *
93 a.a. *
101 a.a. *
177 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2wh4
Name: Ribosome
Title: Insights into translational termination from the structure of rf2 bound to the ribosome
Structure: 23s ribosomal RNA. Chain: a. Other_details: chain a (23s RNA) has e.Coli residue numbering, based on a structural alignment with the corresponding e. Coli structure in 2aw4. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l1. Chain: c.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Atcc: 27634. Atcc: 27634
Resolution:
3.45Å     R-factor:   0.210     R-free:   0.257
Authors: A.Weixlbaumer,H.Jin,C.Neubauer,R.M.Voorhees,S.Petry, A.C.Kelley,V.Ramakrishnan
Key ref:
A.Weixlbaumer et al. (2008). Insights into translational termination from the structure of RF2 bound to the ribosome. Science, 322, 953-956. PubMed id: 18988853 DOI: 10.1126/science.1164840
Date:
30-Apr-09     Release date:   19-May-09    
Supersedes: 2jl8
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60493  (RL27_THET8) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
P60494  (RL28_THET8) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP6  (RL29_THET8) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJE1  (RL31_THET8) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P80339  (RL32_THET8) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
P35871  (RL33_THET8) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
45 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKU1  (RL35_THET8) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHR2  (RL36_THET8) -  50S ribosomal protein L36
Seq:
Struc:
37 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP7  (RL1_THET8) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
191 a.a.
Protein chain
Pfam   ArchSchema ?
P60405  (RL2_THET8) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN8  (RL3_THET8) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN9  (RL4_THET8) -  50S ribosomal protein L4
Seq:
Struc:
210 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ0  (RL5_THET8) -  50S ribosomal protein L5
Seq:
Struc:
182 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ3  (RL6_THET8) -  50S ribosomal protein L6
Seq:
Struc:
180 a.a.
160 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ1  (RL9_THET8) -  50S ribosomal protein L9
Seq:
Struc:
148 a.a.
146 a.a.*
Protein chain
No UniProt id for this chain
Struc: 130 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP6  (RL11_THET8) -  50S ribosomal protein L11
Seq:
Struc:
147 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P60488  (RL13_THET8) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP8  (RL14_THET8) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ7  (RL15_THET8) -  50S ribosomal protein L15
Seq:
Struc:
150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60489  (RL16_THET8) -  50S ribosomal protein L16
Seq:
Struc:
141 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Z9H5  (RL17_THET8) -  50S ribosomal protein L17
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ4  (RL18_THET8) -  50S ribosomal protein L18
Seq:
Struc:
112 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P60490  (RL19_THET8) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P60491  (RL20_THET8) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P60492  (RL21_THET8) -  50S ribosomal protein L21
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP0  (RL23_THET8) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP9  (RL24_THET8) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHZ1  (RL25_THET8) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
177 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     regulation of translation   2 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1126/science.1164840 Science 322:953-956 (2008)
PubMed id: 18988853  
 
 
Insights into translational termination from the structure of RF2 bound to the ribosome.
A.Weixlbaumer, H.Jin, C.Neubauer, R.M.Voorhees, S.Petry, A.C.Kelley, V.Ramakrishnan.
 
  ABSTRACT  
 
The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The structure of RF2 in the ribosome. (A) Unbiased difference Fourier maps showing the density of RF2 in the peptidyl transferase center of the ribosome. (B) Overview of the structure showing the 50S subunit (light blue), the 30S subunit (yellow) with E-site tRNA (red), P-site tRNA (green), and RF2 colored by domains as in (C). The mRNA is shown in magenta. (C) Conformational differences between the isolated crystal structure of RF2 (15) (shown in light blue), and the ribosome-bound form (colored by domains as labeled) are indicated. Loop regions connecting domain 3 with domains 2 and 4, that undergo substantial conformational changes, are highlighted in red.
Figure 4.
Fig. 4. A model of the substrate complex that suggests the basis for catalysis. (A) The interaction of Q240 of RF2 and A2451 of 23S RNA in the current structure. (B) A proposed structure showing how a minor change in the orientation of Q240 would allow it to coordinate a water molecule (transparent orange versus yellow). In gray is a transition-state analog superposed on this structure [1VQ7, taken from (24)] that was used to place the putative water that would take part in a nucleophilic attack on the ester bond. (C) A schematic representation of how a network of interactions among the conserved Q240, the coordinated water molecule that is the attacking nucleophile, the ribose of A76 of P-site tRNA (in C2'-endo conformation), and A2451 would act to facilitate catalysis.
 
  The above figures are reprinted from an Open Access publication published by the AAAs: Science (2008, 322, 953-956) copyright 2008.  
  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.  
  21253384 D.Kurita, A.Muto, and H.Himeno (2011).
tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation.
  J Nucleic Acids, 2011, 130581.  
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.  
21219451 M.Dreyfus, and V.Heurgué-Hamard (2011).
Termination troubles in Escherichia coli K12.
  Mol Microbiol, 79, 288-291.  
21151095 M.Y.Pavlov, A.Zorzet, D.I.Andersson, and M.Ehrenberg (2011).
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits.
  EMBO J, 30, 289-301.  
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.  
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
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
20359191 D.A.Hiller, M.Zhong, V.Singh, and S.A.Strobel (2010).
Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects.
  Biochemistry, 49, 3868-3878.  
20668033 D.E.Burakovsky, P.V.Sergiev, M.A.Steblyanko, A.V.Kubarenko, A.L.Konevega, A.A.Bogdanov, M.V.Rodnina, and O.A.Dontsova (2010).
Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination.
  RNA, 16, 1848-1853.  
20525967 D.Graber, H.Moroder, J.Steger, K.Trappl, N.Polacek, and R.Micura (2010).
Reliable semi-synthesis of hydrolysis-resistant 3'-peptidyl-tRNA conjugates containing genuine tRNA modifications.
  Nucleic Acids Res, 38, 6796-6802.  
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.  
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
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20724456 H.S.Zaher, and R.Green (2010).
Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix.
  RNA, 16, 1980-1989.  
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.  
20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
  Biochem Biophys Res Commun, 393, 1-5.  
20688868 K.N.Bulygin, Y.S.Khairulina, P.M.Kolosov, A.G.Ven'yaminova, D.M.Graifer, Y.N.Vorobjev, L.Y.Frolova, L.L.Kisselev, and G.G.Karpova (2010).
Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome.
  RNA, 16, 1902-1914.  
20974926 K.Saito, K.Kobayashi, M.Wada, I.Kikuno, A.Takusagawa, M.Mochizuki, T.Uchiumi, R.Ishitani, O.Nureki, and K.Ito (2010).
Omnipotent role of archaeal elongation factor 1 alpha (EF1α in translational elongation and termination, and quality control of protein synthesis.
  Proc Natl Acad Sci U S A, 107, 19242-19247.
PDB code: 3agk
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
20631789 M.Ehrenberg (2010).
Protein synthesis: Translocation in slow motion.
  Nature, 466, 325-326.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
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
19965768 S.Kimura, and T.Suzuki (2010).
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
  Nucleic Acids Res, 38, 1341-1352.  
20208546 S.L.He, and R.Green (2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
  Nat Struct Mol Biol, 17, 465-470.  
20699303 S.P.McClory, J.M.Leisring, D.Qin, and K.Fredrick (2010).
Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection.
  RNA, 16, 1925-1934.  
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.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19761774 B.D.Janssen, and C.S.Hayes (2009).
Kinetics of paused ribosome recycling in Escherichia coli.
  J Mol Biol, 394, 251-267.  
19874047 B.Hetrick, K.Lee, and S.Joseph (2009).
Kinetics of stop codon recognition by release factor 1.
  Biochemistry, 48, 11178-11184.  
19933110 B.Seidelt, C.A.Innis, D.N.Wilson, M.Gartmann, J.P.Armache, E.Villa, L.G.Trabuco, T.Becker, T.Mielke, K.Schulten, T.A.Steitz, and R.Beckmann (2009).
Structural insight into nascent polypeptide chain-mediated translational stalling.
  Science, 326, 1412-1415.
PDB codes: 2wwl 2wwq
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
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
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.  
19129838 K.Fredrick, and M.Ibba (2009).
Protein synthesis: Errors rectified in retrospect.
  Nature, 457, 157-158.  
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.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19363482 R.M.Voorhees, A.Weixlbaumer, D.Loakes, A.C.Kelley, and V.Ramakrishnan (2009).
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
  Nat Struct Mol Biol, 16, 528-533.
PDB codes: 2wdg 2wdh 2wdi 2wdj 2wdk 2wdl 2wdm 2wdn
19329641 R.Yang, L.R.Cruz-Vera, and C.Yanofsky (2009).
23S rRNA nucleotides in the peptidyl transferase center are essential for tryptophanase operon induction.
  J Bacteriol, 191, 3445-3450.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
19417105 Z.Cheng, K.Saito, A.V.Pisarev, M.Wada, V.P.Pisareva, T.V.Pestova, M.Gajda, A.Round, C.Kong, M.Lim, Y.Nakamura, D.I.Svergun, K.Ito, and H.Song (2009).
Structural insights into eRF3 and stop codon recognition by eRF1.
  Genes Dev, 23, 1106-1118.
PDB codes: 3e1y 3e20
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.