7D43

eIF2B-eIF2(aP), aPg complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaA, B305Homo sapiensMutation(s): 0 
Gene Names: EIF2B1EIF2BA
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Find proteins for Q14232 (Homo sapiens)
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PHAROS:  Q14232
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit betaC, D351Homo sapiensMutation(s): 0 
Gene Names: EIF2B2EIF2BB
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Find proteins for P49770 (Homo sapiens)
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PHAROS:  P49770
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaE, F452Homo sapiensMutation(s): 0 
Gene Names: EIF2B3
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Find proteins for Q9NR50 (Homo sapiens)
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PHAROS:  Q9NR50
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaG, H523Homo sapiensMutation(s): 0 
Gene Names: EIF2B4EIF2BD
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Find proteins for Q9UI10 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilonI, J721Homo sapiensMutation(s): 0 
Gene Names: EIF2B5EIF2BE
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Find proteins for Q13144 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1K, L315Homo sapiensMutation(s): 0 
Gene Names: EIF2S1EIF2A
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Find proteins for P05198 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 2M333Homo sapiensMutation(s): 0 
Gene Names: EIF2S2EIF2B
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Find proteins for P20042 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3N [auth P]472Homo sapiensMutation(s): 0 
Gene Names: EIF2S3EIF2G
EC: 3.6.5.3
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Find proteins for P41091 (Homo sapiens)
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
K, LL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-09-22 
  • Released Date: 2020-12-09 
  • Deposition Author(s): Kashiwagi, K., Ito, T.

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