9HVD | pdb_00009hvd

Native human P-eIF2-eIF2B complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Termination of the integrated stress response.

De Miguel, C.Thorkelsson, S.R.Fatalska, A.Hodgson, G.Wang, C.Bertolotti, A.

(2025) Science : eadw5137-eadw5137

  • DOI: https://doi.org/10.1126/science.adw5137
  • Primary Citation of Related Structures:  
    9HVD, 9HVE, 9HVF

  • PubMed Abstract: 

    Stress responses enable cells to detect, adapt to, and survive challenges. The benefit of these signaling pathways depends on their reversibility. The integrated stress response (ISR) is elicited by phosphorylation of translation initiation factor eIF2, which traps and inhibits rate-limiting translation factor eIF2B thereby attenuating translation initiation. Termination of this pathway thus requires relieving eIF2B from P-eIF2 inhibition. Here, we found that eIF2 phosphatase subunits PPP1R15A and PPP1R15B (R15B) bound P-eIF2 in complex with eIF2B. Biochemical investigations guided by cryo-EM structures of native eIF2-eIF2B and P-eIF2-eIF2B complexes bound to R15B demonstrated that R15B enabled dephosphorylation of otherwise dephosphorylation-incompetent P-eIF2 on eIF2B. This sheds light on ISR termination, revealing that R15B rescues eIF2B from P-eIF2 inhibition, thereby safeguarding translation and cell fitness.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaA [auth F],
G [auth E]
452Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR50 (Homo sapiens)
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PHAROS:  Q9NR50
GTEx:  ENSG00000070785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR50
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1B [auth K],
L
315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05198 (Homo sapiens)
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PHAROS:  P05198
GTEx:  ENSG00000134001 
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UniProt GroupP05198
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF2B subunit epsilonC [auth J],
H [auth I]
721Homo sapiensMutation(s): 0 
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Find proteins for Q13144 (Homo sapiens)
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PHAROS:  Q13144
GTEx:  ENSG00000145191 
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UniProt GroupQ13144
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF2B subunit betaD,
I [auth C]
351Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens)
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PHAROS:  P49770
GTEx:  ENSG00000119718 
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UniProt GroupP49770
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaE [auth B],
J [auth A]
305Homo sapiensMutation(s): 0 
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Find proteins for Q14232 (Homo sapiens)
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PHAROS:  Q14232
GTEx:  ENSG00000111361 
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UniProt GroupQ14232
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaF [auth G],
K [auth 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 
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UniProt GroupQ9UI10
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B [auth K],
L
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105185860
Wellcome TrustUnited Kingdom206367/Z/ 17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references