Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44985.41 
• Atom Count: 3049 
• Residue Count: 410 
• Unique protein chains: 1

1KJZ

Structure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant

• DOI: 10.2210/pdb1KJZ/pdb

• Classification: TRANSLATION
• Organism(s): Pyrococcus abyssi (strain GE5 / Orsay)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2001-12-06 Released: 2002-04-10 
• Deposition Author(s): Schmitt, E., Blanquet, S., Mechulam, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.225 

Literature

The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.

Schmitt, E., Blanquet, S., Mechulam, Y.

(2002) EMBO J. 21: 1821-1832

• PubMed: 11927566 
• DOI: 10.1093/emboj/21.7.1821
• Primary Citation of Related Structures:  
  1KK3, 1KK2, 1KK1, 1KK0


• PubMed Abstract: 
  

The heterotrimeric factor e/aIF2 plays a central role in eukaryotic/archaeal initiation of translation. By delivering the initiator methionyl-tRNA to the ribosome, e/aIF2 ensures specificity of initiation codon selection. The three subunits of aIF2 from the hyperthermophilic archaeon Pyrococcus abyssi could be overproduced in Escherichia coli. The beta and gamma subunits each contain a tightly bound zinc. The large gamma subunit is shown to form the structural core for trimer assembly. The crystal structures of aIF2gamma, free or complexed to GDP-Mg(2+) or GDPNP-Mg(2+), were resolved at resolutions better than 2 A. aIF2gamma displays marked similarities to elongation factors. A distinctive feature of e/aIF2gamma is a subdomain containing a zinc-binding knuckle. Examination of the nucleotide-complexed aIF2gamma structures suggests mechanisms of action and tRNA binding properties similar to those of an elongation factor. Implications for the mechanism of translation initiation in both eukarya and archaea are discussed. In particular, positioning of the initiator tRNA in the ribosomal A site during the search for the initiation codon is envisaged.

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Organizational Affiliation: 

Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
eIF2gamma	A	410	Pyrococcus abyssi (strain GE5 / Orsay)	Mutation(s): 1  Gene Names: eif2g (aif2G)
Find proteins for Q9V1G0 (Pyrococcus abyssi (strain GE5 / Orsay)) Go to UniProtKB:  Q9V1G0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 51.480	α = 90.00
b = 86.741	β = 110.40
c = 58.083	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-06 
• Released Date: 2002-04-10 
• Deposition Author(s): Schmitt, E., Blanquet, S., Mechulam, Y.

Revision History 

• Version 1.0: 2002-04-10
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance