6EZO

Eukaryotic initiation factor EIF2B in complex with ISRIB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B.

Zyryanova, A.F.Weis, F.Faille, A.Alard, A.A.Crespillo-Casado, A.Sekine, Y.Harding, H.P.Allen, F.Parts, L.Fromont, C.Fischer, P.M.Warren, A.J.Ron, D.

(2018) Science 359: 1533-1536

  • DOI: https://doi.org/10.1126/science.aar5129
  • Primary Citation of Related Structures:  
    6EZO

  • PubMed Abstract: 

    The integrated stress response (ISR) is a conserved translational and transcriptional program affecting metabolism, memory, and immunity. The ISR is mediated by stress-induced phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) that attenuates the guanine nucleotide exchange factor eIF2B. A chemical inhibitor of the ISR, ISRIB, reverses the attenuation of eIF2B by phosphorylated eIF2α, protecting mice from neurodegeneration and traumatic brain injury. We describe a 4.1-angstrom-resolution cryo-electron microscopy structure of human eIF2B with an ISRIB molecule bound at the interface between the β and δ regulatory subunits. Mutagenesis of residues lining this pocket altered the hierarchical cellular response to ISRIB analogs in vivo and ISRIB binding in vitro. Our findings point to a site in eIF2B that can be exploited by ISRIB to regulate translation.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK. az310@cam.ac.uk ajw1000@cam.ac.uk dr360@medschl.cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alpha
A, B
305Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14232 (Homo sapiens)
Explore Q14232 
Go to UniProtKB:  Q14232
PHAROS:  Q14232
GTEx:  ENSG00000111361 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14232
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit beta
C, D
373Homo sapiensMutation(s): 0 
Gene Names: EIF2B2EIF2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens)
Explore P49770 
Go to UniProtKB:  P49770
PHAROS:  P49770
GTEx:  ENSG00000119718 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49770
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gamma
E, F
452Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR50 (Homo sapiens)
Explore Q9NR50 
Go to UniProtKB:  Q9NR50
PHAROS:  Q9NR50
GTEx:  ENSG00000070785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR50
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit delta
G, H
523Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI10 (Homo sapiens)
Explore Q9UI10 
Go to UniProtKB:  Q9UI10
PHAROS:  Q9UI10
GTEx:  ENSG00000115211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Human eukaryotic initiation factor EIF2B epsilon subunits
I, J
721Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13144 (Homo sapiens)
Explore Q13144 
Go to UniProtKB:  Q13144
PHAROS:  Q13144
GTEx:  ENSG00000145191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13144
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C7B
Query on C7B

Download Ideal Coordinates CCD File 
K [auth D]2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
C22 H24 Cl2 N2 O4
HJGMCDHQPXTGAV-IYARVYRRSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT200848/Z/16/Z
Medical Research Council (United Kingdom)United KingdomRG67621

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other, Structure summary
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references