spacer
spacer

PDBsum entry 3e20
Go to PDB code: 
protein Protein-protein interface(s) links
Translation PDB id
3e20

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
196 a.a. *
261 a.a. *
175 a.a. *
* Residue conservation analysis
PDB id:
3e20
Name: Translation
Title: Crystal structure of s.Pombe erf1/erf3 complex
Structure: Eukaryotic peptide chain release factor gtp-binding subunit. Chain: a, d, e, j. Fragment: unp residues 467-662. Synonym: erf2, erf-3, erf3, translation release factor 3, polypeptide release factor 3, sup35. Engineered: yes. Eukaryotic peptide chain release factor subunit 1. Chain: c, b, h, k.
Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: sup35, spcc584.04. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: sup45, spac1834.01.
Resolution:
3.50Å     R-factor:   0.259     R-free:   0.280
Authors: Z.Cheng,M.Lim,C.Kong,H.Song
Key ref: Z.Cheng et al. (2009). Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev, 23, 1106-1118. PubMed id: 19417105
Date:
05-Aug-08     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O74718  (ERF3_SCHPO) -  Eukaryotic peptide chain release factor GTP-binding subunit from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Seq:
Struc: 		 
Seq:
Struc: 		662 a.a.
196 a.a.
Protein chains
Pfam   ArchSchema ?
P79063  (ERF1_SCHPO) -  Eukaryotic peptide chain release factor subunit 1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Seq:
Struc: 		433 a.a.
261 a.a.
Protein chains
Pfam   ArchSchema ?
P79063  (ERF1_SCHPO) -  Eukaryotic peptide chain release factor subunit 1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Seq:
Struc: 		433 a.a.
175 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 41 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, D, E, J: E.C.3.6.5.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Genes Dev 23:1106-1118 (2009)
PubMed id: 19417105  
 
 
Structural insights into eRF3 and stop codon recognition by eRF1.
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, H.Song.
 
  ABSTRACT  
 
Eukaryotic translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. The crystal structures of human and Schizosaccharomyces pombe full-length eRF1 in complex with eRF3 lacking the GTPase domain revealed details of the interaction between these two factors and marked conformational changes in eRF1 that occur upon binding to eRF3, leading eRF1 to resemble a tRNA molecule. Small-angle X-ray scattering analysis of the eRF1/eRF3/GTP complex suggested that eRF1's M domain contacts eRF3's GTPase domain. Consistently, mutation of Arg192, which is predicted to come in close contact with the switch regions of eRF3, revealed its important role for eRF1's stimulatory effect on eRF3's GTPase activity. An ATP molecule used as a crystallization additive was bound in eRF1's putative decoding area. Mutational analysis of the ATP-binding site shed light on the mechanism of stop codon recognition by eRF1.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23072885 M.Graille, and B.Séraphin (2012).
Surveillance pathways rescuing eukaryotic ribosomes lost in translation.
  Nat Rev Mol Cell Biol, 13, 727-735.  
23072888 S.Kervestin, and A.Jacobson (2012).
NMD: a multifaceted response to premature translational termination.
  Nat Rev Mol Cell Biol, 13, 700-712.  
20860996 B.Eliseev, P.Kryuchkova, E.Alkalaeva, and L.Frolova (2011).
A single amino acid change of translation termination factor eRF1 switches between bipotent and omnipotent stop-codon specificity.
  Nucleic Acids Res, 39, 599-608.  
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
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
21448132 V.P.Pisareva, M.A.Skabkin, C.U.Hellen, T.V.Pestova, and A.V.Pisarev (2011).
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes.
  EMBO J, 30, 1804-1817.  
20553496 A.B.Mantsyzov, E.V.Ivanova, B.Birdsall, E.Z.Alkalaeva, P.N.Kryuchkova, G.Kelly, L.Y.Frolova, and V.I.Polshakov (2010).
NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor.
  FEBS J, 277, 2611-2627.
PDB code: 2ktv
21102444 A.M.van den Elzen, J.Henri, N.Lazar, M.E.Gas, D.Durand, F.Lacroute, M.Nicaise, H.van Tilbeurgh, B.Séraphin, and M.Graille (2010).
Dissection of Dom34-Hbs1 reveals independent functions in two RNA quality control pathways.
  Nat Struct Mol Biol, 17, 1446-1452.
PDB codes: 3p26 3p27
19906736 A.V.Kononenko, V.A.Mitkevich, G.C.Atkinson, T.Tenson, V.I.Dubovaya, L.Y.Frolova, A.A.Makarov, and V.Hauryliuk (2010).
GTP-dependent structural rearrangement of the eRF1:eRF3 complex and eRF3 sequence motifs essential for PABP binding.
  Nucleic Acids Res, 38, 548-558.  
20122402 A.V.Pisarev, M.A.Skabkin, V.P.Pisareva, O.V.Skabkina, A.M.Rakotondrafara, M.W.Hentze, C.U.Hellen, and T.V.Pestova (2010).
The role of ABCE1 in eukaryotic posttermination ribosomal recycling.
  Mol Cell, 37, 196-210.  
20876129 K.Kobayashi, I.Kikuno, K.Kuroha, K.Saito, K.Ito, R.Ishitani, T.Inada, and O.Nureki (2010).
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.
  Proc Natl Acad Sci U S A, 107, 17575-17579.
PDB codes: 3agj 3wxm
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
20955199 L.Bidou, J.P.Rousset, and O.Namy (2010).
Translational errors: from yeast to new therapeutic targets.
  FEMS Yeast Res, 10, 1070-1082.  
20890290 L.Chen, D.Muhlrad, V.Hauryliuk, Z.Cheng, M.K.Lim, V.Shyp, R.Parker, and H.Song (2010).
Structure of the Dom34-Hbs1 complex and implications for no-go decay.
  Nat Struct Mol Biol, 17, 1233-1240.
PDB code: 3mca
20136636 Y.Wang, B.Chai, W.Wang, and A.Liang (2010).
Functional characterization of polypeptide release factor 1b in the ciliate Euplotes.
  Biosci Rep, 30, 425-431.  
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.

 

spacer
spacer