1DT9

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

• PDB DOI:  https://doi.org/10.2210/pdb1DT9/pdb

• Classification: TRANSLATION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2000-01-12 Released: 2000-02-02 
• Deposition Author(s): Frolova, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.314 
• R-Value Work: 0.246 

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

• PubMed: 10676813 
• DOI: https://doi.org/10.1016/s0092-8674(00)80667-4
• Primary Citation of 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.

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Related Citations: 

• Mutations in the Highly Conserved GGQ Motif of Class 1 Polypeptide Release Factors Abolish Ability of Human eRF1 to Trigger Peptidyl-tRNA Hydrolysis.
  Frolova, L.Y., Tsivkovskii, R.Y., Sivolobova, G.F., Oparina, N.Y., Serpinsky, O.I., Blinov, V.M., Tatkov, S.I., Kisselev, L.L.
  (1999) RNA 5: 1014

• A Highly Conserved Eukaryotic Protein Family Possesing Properties of Polypeptide Chain Release Factor
  Frolova, L., Le Goff, X., Rasmussen, H.H., Cheperegin, S., Drugeon, G., Kress, M., Arman, I., Haenni, A.L., Celis, J.E., Philippe, M., Justesen, J., Kisselev, L.
  (1994) Nature 372: 701

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Organizational Affiliation: 

Section of Structural Biology, Institute of Cancer Research, London, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1)	A	437	Homo sapiens	Mutation(s): 0  Gene Names: ETF1, ERF1, RF1, SUP45L1
UniProt & NIH Common Fund Data Resources
Find proteins for P62495 (Homo sapiens) Explore P62495  Go to UniProtKB:  P62495
PHAROS:  P62495

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.314 
• R-Value Work: 0.246 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.08	α = 90
b = 77.08	β = 90
c = 194.44	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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