7D45

eIF2B-eIF2(aP), aP1 complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B.

Zyryanova, A.F., Kashiwagi, K., Rato, C., Harding, H.P., Crespillo-Casado, A., Perera, L.A., Sakamoto, A., Nishimoto, M., Yonemochi, M., Shirouzu, M., Ito, T., Ron, D.

(2021) Mol Cell 81: 88

  • DOI: 10.1016/j.molcel.2020.10.031
  • Primary Citation of Related Structures:  
    7D43, 7D44, 7D45, 7D46

  • PubMed Abstract: 

    • The small molecule ISRIB antagonizes the activation of the integrated stress response (ISR) by phosphorylated translation initiation factor 2, eIF2(αP). ISRIB and eIF2(αP) bind distinct sites in their common target, eIF2B, a guanine nucleotide exchange factor for eIF2 ...

    The small molecule ISRIB antagonizes the activation of the integrated stress response (ISR) by phosphorylated translation initiation factor 2, eIF2(αP). ISRIB and eIF2(αP) bind distinct sites in their common target, eIF2B, a guanine nucleotide exchange factor for eIF2. We have found that ISRIB-mediated acceleration of eIF2B's nucleotide exchange activity in vitro is observed preferentially in the presence of eIF2(αP) and is attenuated by mutations that desensitize eIF2B to the inhibitory effect of eIF2(αP). ISRIB's efficacy as an ISR inhibitor in cells also depends on presence of eIF2(αP). Cryoelectron microscopy (cryo-EM) showed that engagement of both eIF2B regulatory sites by two eIF2(αP) molecules remodels both the ISRIB-binding pocket and the pockets that would engage eIF2α during active nucleotide exchange, thereby discouraging both binding events. In vitro, eIF2(αP) and ISRIB reciprocally opposed each other's binding to eIF2B. These findings point to antagonistic allostery in ISRIB action on eIF2B, culminating in inhibition of the ISR.

    Organizational Affiliation: 

    Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge CB2 0XY, UK. Electronic address: dr360@medschl.cam.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaA, B305Homo sapiensMutation(s): 0 
Gene Names: EIF2B1, EIF2BA
UniProt & NIH Common Fund Data Resources
Find proteins for Q14232 (Homo sapiens)
Explore Q14232 
Go to UniProtKB:  Q14232
PHAROS:  Q14232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14232
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit betaC, D351Homo sapiensMutation(s): 0 
Gene Names: EIF2B2, EIF2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens)
Explore P49770 
Go to UniProtKB:  P49770
PHAROS:  P49770
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49770
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaE, F452Homo sapiensMutation(s): 0 
Gene Names: EIF2B3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR50 (Homo sapiens)
Explore Q9NR50 
Go to UniProtKB:  Q9NR50
PHAROS:  Q9NR50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR50
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaG, H523Homo sapiensMutation(s): 0 
Gene Names: EIF2B4, EIF2BD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI10 (Homo sapiens)
Explore Q9UI10 
Go to UniProtKB:  Q9UI10
PHAROS:  Q9UI10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI10
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilonI, J721Homo sapiensMutation(s): 0 
Gene Names: EIF2B5, EIF2BE
UniProt & NIH Common Fund Data Resources
Find proteins for Q13144 (Homo sapiens)
Explore Q13144 
Go to UniProtKB:  Q13144
PHAROS:  Q13144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13144
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1K315Homo sapiensMutation(s): 0 
Gene Names: EIF2S1, EIF2A
UniProt & NIH Common Fund Data Resources
Find proteins for P05198 (Homo sapiens)
Explore P05198 
Go to UniProtKB:  P05198
PHAROS:  P05198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05198
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		K L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references