5B04

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of eukaryotic translation initiation factor 2B

Kashiwagi, K.Takahashi, M.Nishimoto, M.Hiyama, T.B.Higo, T.Umehara, T.Sakamoto, K.Ito, T.Yokoyama, S.

(2016) Nature 531: 47-52

  • DOI: 10.1038/nature16991

  • PubMed Abstract: 
  • Eukaryotic cells restrict protein synthesis under various stress conditions, by inhibiting the eukaryotic translation initiation factor 2B (eIF2B). eIF2B is the guanine nucleotide exchange factor for eIF2, a heterotrimeric G protein consisting of α-, ...

    Eukaryotic cells restrict protein synthesis under various stress conditions, by inhibiting the eukaryotic translation initiation factor 2B (eIF2B). eIF2B is the guanine nucleotide exchange factor for eIF2, a heterotrimeric G protein consisting of α-, β- and γ-subunits. eIF2B exchanges GDP for GTP on the γ-subunit of eIF2 (eIF2γ), and is inhibited by stress-induced phosphorylation of eIF2α. eIF2B is a heterodecameric complex of two copies each of the α-, β-, γ-, δ- and ε-subunits; its α-, β- and δ-subunits constitute the regulatory subcomplex, while the γ- and ε-subunits form the catalytic subcomplex. The three-dimensional structure of the entire eIF2B complex has not been determined. Here we present the crystal structure of Schizosaccharomyces pombe eIF2B with an unprecedented subunit arrangement, in which the α2β2δ2 hexameric regulatory subcomplex binds two γε dimeric catalytic subcomplexes on its opposite sides. A structure-based in vitro analysis by a surface-scanning site-directed photo-cross-linking method identified the eIF2α-binding and eIF2γ-binding interfaces, located far apart on the regulatory and catalytic subcomplexes, respectively. The eIF2γ-binding interface is located close to the conserved 'NF motif', which is important for nucleotide exchange. A structural model was constructed for the complex of eIF2B with phosphorylated eIF2α, which binds to eIF2B more strongly than the unphosphorylated form. These results indicate that the eIF2α phosphorylation generates the 'nonproductive' eIF2-eIF2B complex, which prevents nucleotide exchange on eIF2γ, and thus provide a structural framework for the eIF2B-mediated mechanism of stress-induced translational control.


    Organizational Affiliation

    Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit alpha
A, B
341Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: tif221
Find proteins for Q9USP0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USP0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable translation initiation factor eIF-2B subunit beta
C, D
399Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: tif222
Find proteins for Q9UT76 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9UT76
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Probable translation initiation factor eIF-2B subunit gamma
E, F
458Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 3 
Gene Names: tif223
Find proteins for P56288 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P56288
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Probable translation initiation factor eIF-2B subunit delta
G, H
467Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: tif224
Find proteins for Q09924 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q09924
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Probable translation initiation factor eIF-2B subunit epsilon
I, J
678Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: tif225
Find proteins for P56287 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P56287
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, G, H, I
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 144.495α = 90.00
b = 209.234β = 90.00
c = 223.534γ = 90.00
Software Package:
Software NamePurpose
XDSphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Advisory, Data collection, Database references, Derived calculations