9HVF | pdb_00009hvf

Native human PPP1R15B-P-eIF2-eIF2B complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 E]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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 1 regulatory subunit 15BB [auth A]109Homo sapiensMutation(s): 0 
Gene Names: PPP1R15B
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SWA1 (Homo sapiens)
Explore Q5SWA1 
Go to UniProtKB:  Q5SWA1
PHAROS:  Q5SWA1
GTEx:  ENSG00000158615 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SWA1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 2333Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20042 (Homo sapiens)
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Go to UniProtKB:  P20042
PHAROS:  P20042
GTEx:  ENSG00000125977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20042
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3472Homo sapiensMutation(s): 0 
EC: 3.6.5.3
UniProt & NIH Common Fund Data Resources
Find proteins for P41091 (Homo sapiens)
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PHAROS:  P41091
GTEx:  ENSG00000130741 
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UniProt GroupP41091
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1E [auth B]315Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05198 (Homo sapiens)
Explore P05198 
Go to UniProtKB:  P05198
PHAROS:  P05198
GTEx:  ENSG00000134001 
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UniProt GroupP05198
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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