2D74

Crystal structure of translation initiation factor aIF2betagamma heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region.

Sokabe, M.Yao, M.Sakai, N.Toya, S.Tanaka, I.

(2006) Proc Natl Acad Sci U S A 103: 13016-13021

  • DOI: 10.1073/pnas.0604165103
  • Primary Citation of Related Structures:  
    2D74, 2DCU

  • PubMed Abstract: 
  • Archaeal/eukaryotic initiation factor 2 (a/eIF2) consists of alpha-, beta-, and gamma-subunits and delivers initiator methionine tRNA (Met-tRNA(i)) to a small ribosomal subunit in a GTP-dependent manner. The structures of the aIF2betagamma (archaeal initiation factor 2 betagamma) heterodimeric complex in the apo and GDP forms were analyzed at 2 ...

    Archaeal/eukaryotic initiation factor 2 (a/eIF2) consists of alpha-, beta-, and gamma-subunits and delivers initiator methionine tRNA (Met-tRNA(i)) to a small ribosomal subunit in a GTP-dependent manner. The structures of the aIF2betagamma (archaeal initiation factor 2 betagamma) heterodimeric complex in the apo and GDP forms were analyzed at 2.8- and 3.4-A resolution, respectively. The results showed that the N-terminal helix and the central helix-turn-helix domain of the beta-subunit bind to the G domain of the gamma-subunit but are distant from domains 2 and 3, to which the alpha-subunit and Met-tRNA(i) bind. This result is consistent with most of the previous analyses of eukaryotic factors, and thus indicates that the binding mode is essentially conserved among a/eIF2. Comparison with the uncomplexed structure showed significant differences between the two forms of the beta-subunit, particularly the C-terminal zinc-binding domain, which does not interact with the gamma-subunit and was suggested previously to be involved in GTP hydrolysis. Furthermore, the switch 1 region in the gamma-subunit, which is shown to be responsible for Met-tRNA(i) binding by mutational analysis, is moved away from the nucleotide through the interaction with highly conserved R87 in the beta-subunit. These results implicate that conformational change of the beta-subunit facilitates GTP hydrolysis by inducing the conformational change of the switch 1 region toward the off state.


    Organizational Affiliation

    Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 2 gamma subunitA419Pyrococcus furiosus DSM 3638Mutation(s): 1 
Gene Names: PF1717eif2g
EC: 3.6.5.3
Find proteins for Q8U082 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U082 
Go to UniProtKB:  Q8U082
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 2 beta subunitB148Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0481eif2b
Find proteins for Q8U3I5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3I5 
Go to UniProtKB:  Q8U3I5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.467α = 90
b = 76.177β = 90
c = 98.21γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance