3WJ9 | pdb_00003wj9

Crystal structure of the eukaryotic initiation factor

• PDB DOI: https://doi.org/10.2210/pdb3WJ9/pdb

• Classification: TRANSLATION
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-07 Released: 2014-03-12 
• Deposition Author(s): Kashiwagi, K., Ito, T., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.258 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Crystal structure of the eukaryotic translation initiation factor 2A from Schizosaccharomyces pombe.

Kashiwagi, K., Ito, T., Yokoyama, S.

(2014) J Struct Funct Genomics 15: 125-130

• PubMed: 24569939 
• DOI: https://doi.org/10.1007/s10969-014-9177-y
• Primary Citation Related Structures: 
  3WJ9


• PubMed Abstract: 
  

  The eukaryotic translation initiation factor 2A (eIF2A) was identified as a factor that stimulates the binding of methionylated initiator tRNA (Met-tRNA i (Met) ) to the 40S ribosomal subunit, but its physiological role remains poorly defined. Recently, eIF2A was shown to be involved in unconventional translation initiation from CUG codons and in viral protein synthesis under stress conditions where eIF2 is inactivated. We determined the crystal structure of the WD-repeat domain of Schizosaccharomyces pombe eIF2A at 2.5 Å resolution. The structure adopts a novel nine-bladed β-propeller fold. In contrast to the usual β-propeller proteins, the central channel of the molecule has the narrower opening on the bottom of the protein and the wider opening on the top. Highly conserved residues are concentrated in the positively-charged top face, suggesting the importance of this face for interactions with nucleic acids or other initiation factors.

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Organizational Affiliation: 
• Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.29 kDa 
• Atom Count: 6,338 
• Modeled Residue Count: 798 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2A	A, B	412	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: SPBC4B4.04
UniProt
Find proteins for O74965 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O74965  Go to UniProtKB:  O74965

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.258 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.443	α = 90
b = 93.443	β = 90
c = 269.387	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Kashiwagi, K., Ito, T., Yokoyama, S.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary