1DT9 | pdb_00001dt9

THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MECHANISM OF STOP CODON RECOGNITION AND PEPTIDYL-TRNA HYDROLYSIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.314 (Depositor) 
  • R-Value Work: 
    0.246 (Depositor), 0.273 (DCC) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis.

Song, H., Mugnier, P., Das, A.K., Webb, H.M., Evans, D.R., Tuite, M.F., Hemmings, B.A., Barford, D.

(2000) Cell 100: 311-321

  • DOI: https://doi.org/10.1016/s0092-8674(00)80667-4
  • Primary Citation Related Structures: 
    1DT9

  • PubMed Abstract: 

    The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 to 2.8 A resolution, combined with mutagenesis analyses of the universal GGQ motif, reveals the molecular mechanism of release factor activity. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase center. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site.

    • Organizational Affiliation: 
    • Section of Structural Biology, Institute of Cancer Research, London, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 49.09 kDa 
  • Atom Count: 3,241 
  • Modeled Residue Count: 398 
  • Deposited Residue Count: 437 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1)437Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62495 (Homo sapiens)
Explore P62495 
Go to UniProtKB:  P62495
PHAROS:  P62495
GTEx:  ENSG00000120705 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62495
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.314 (Depositor) 
  • R-Value Work:  0.246 (Depositor), 0.273 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.08α = 90
b = 77.08β = 90
c = 194.44γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2000-02-02 
    • Deposition Author(s): Frolova, L.

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references