7KMF

Sugar phosphate activation of the stress sensor eIF2B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sugar phosphate activation of the stress sensor eIF2B.

Hao, Q.Heo, J.M.Nocek, B.P.Hicks, K.G.Stoll, V.S.Remarcik, C.Hackett, S.LeBon, L.Jain, R.Eaton, D.Rutter, J.Wong, Y.L.Sidrauski, C.

(2021) Nat Commun 12: 3440-3440

  • DOI: https://doi.org/10.1038/s41467-021-23836-z
  • Primary Citation of Related Structures:  
    7KMA, 7KMF

  • PubMed Abstract: 

    The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.


  • Organizational Affiliation

    Calico Life Sciences LLC, South San Francisco, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit betaA [auth C],
B [auth D]
367Homo sapiensMutation(s): 0 
Gene Names: EIF2B2EIF2BB
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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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaC [auth F],
D [auth E]
523Homo sapiensMutation(s): 0 
Gene Names: EIF2B4EIF2BD
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Find proteins for Q9UI10 (Homo sapiens)
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PHAROS:  Q9UI10
GTEx:  ENSG00000115211 
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UniProt GroupQ9UI10
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaE [auth H],
F [auth G]
377Homo sapiensMutation(s): 0 
Gene Names: EIF2B1EIF2BA
UniProt & NIH Common Fund Data Resources
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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilonG [auth B],
H [auth I]
721Homo sapiensMutation(s): 0 
Gene Names: EIF2B5EIF2BE
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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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaI [auth J],
J [auth K]
452Homo sapiensMutation(s): 0 
Gene Names: EIF2B3
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Find proteins for Q9NR50 (Homo sapiens)
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PHAROS:  Q9NR50
GTEx:  ENSG00000070785 
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UniProt GroupQ9NR50
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15
MODEL REFINEMENTPHENIXdev_3916

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Refinement description, Structure summary