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 7TRJ | pdb_00007trj

The eukaryotic translation initiation factor 2B from Homo sapiens with a H160D mutation in the beta subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7TRJ

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

Literature

A point mutation in the nucleotide exchange factor eIF2B constitutively activates the integrated stress response by allosteric modulation.

Boone, M., Wang, L., Lawrence, R., Frost, A., Walter, P., Schoof, M.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.76171
  • Primary Citation Related Structures: 
    7TRJ

  • PubMed Abstract: 

    In eukaryotic cells, stressors reprogram the cellular proteome by activating the integrated stress response (ISR). In its canonical form, stress-sensing kinases phosphorylate the eukaryotic translation initiation factor eIF2 (eIF2-P), which ultimately leads to reduced levels of ternary complex required for initiation of mRNA translation. Previously we showed that translational control is primarily exerted through a conformational switch in eIF2's nucleotide exchange factor, eIF2B, which shifts from its active A-State conformation to its inhibited I-State conformation upon eIF2-P binding, resulting in reduced nucleotide exchange on eIF2 (Schoof et al. 2021). Here, we show functionally and structurally how a single histidine to aspartate point mutation in eIF2B's β subunit (H160D) mimics the effects of eIF2-P binding by promoting an I-State like conformation, resulting in eIF2-P independent activation of the ISR. These findings corroborate our previously proposed A/I-State model of allosteric ISR regulation.


  • Organizational Affiliation: 
    • Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, United States.

Macromolecule Content 

  • Total Structure Weight: 522.36 kDa 
  • Atom Count: 25,190 
  • Modeled Residue Count: 3,234 
  • Deposited Residue Count: 4,704 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilonA,
F [auth B]
721Homo 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
GTEx:  ENSG00000145191 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13144
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit betaB [auth D],
G [auth C]
351Homo sapiensMutation(s): 1 
Gene Names: EIF2B2, EIF2BB
UniProt & NIH Common Fund Data Resources
Find proteins for P49770 (Homo sapiens)
Explore P49770 
Go to UniProtKB:  P49770
PHAROS:  P49770
GTEx:  ENSG00000119718 
Entity Groups
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UniProt GroupP49770
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaC [auth E],
H [auth F]
523Homo 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
GTEx:  ENSG00000115211 
Entity Groups
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UniProt GroupQ9UI10
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaD [auth G],
I [auth H]
305Homo 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
GTEx:  ENSG00000111361 
Entity Groups
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UniProt GroupQ14232
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaE [auth I],
J
452Homo 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
GTEx:  ENSG00000070785 
Entity Groups
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UniProt GroupQ9NR50
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection