1G7R

X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding.

Roll-Mecak, A.Cao, C.Dever, T.E.Burley, S.K.

(2000) Cell 103: 781-792

  • DOI: https://doi.org/10.1016/s0092-8674(00)00181-1
  • Primary Citation of Related Structures:  
    1G7R, 1G7S, 1G7T

  • PubMed Abstract: 

    X-ray structures of the universal translation initiation factor IF2/eIF5B have been determined in three states: free enzyme, inactive IF2/eIF5B.GDP, and active IF2/eIF5B.GTP. The "chalice-shaped" enzyme is a GTPase that facilitates ribosomal subunit joining and Met-tRNA(i) binding to ribosomes in all three kingdoms of life. The conserved core of IF2/eIF5B consists of an N-terminal G domain (I) plus an EF-Tu-type beta barrel (II), followed by a novel alpha/beta/alpha-sandwich (III) connected via an alpha helix to a second EF-Tu-type beta barrel (IV). Structural comparisons reveal a molecular lever, which amplifies a modest conformational change in the Switch 2 region of the G domain induced by Mg(2+)/GTP binding over a distance of 90 A from the G domain active center to domain IV. Mechanisms of GTPase function and ribosome binding are discussed.


  • Organizational Affiliation

    Laboratories of Molecular Biophysics The Rockefeller University 10021, New York, NY 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSLATION INITIATION FACTOR IF2/EIF5B594Methanothermobacter thermautotrophicusMutation(s): 19 
UniProt
Find proteins for O26359 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26359 
Go to UniProtKB:  O26359
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26359
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.316α = 104.9
b = 54.355β = 101.33
c = 90.978γ = 98.75
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-06
    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: 2018-02-14
    Changes: Experimental preparation
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary