6QG5

Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model C)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the inhibition of translation through eIF2 alpha phosphorylation.

Gordiyenko, Y.Llacer, J.L.Ramakrishnan, V.

(2019) Nat Commun 10: 2640-2640

  • DOI: 10.1038/s41467-019-10606-1
  • Primary Citation of Related Structures:  
    6QG5, 6QG6, 6QG1, 6QG0, 6QG3, 6QG2

  • PubMed Abstract: 
  • One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B ...

    One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58-63 with eIF2Bδ leading to a competition with Met-tRNA i .


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alphaA, B305Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCN3AAS2TIF221YKR026C
UniProt
Find proteins for P14741 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit betaC, D381Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD7TIF222YLR291CL8003.17
UniProt
Find proteins for P32502 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gammaE, F578Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD1TIF223TRA3YOR260W
UniProt
Find proteins for P09032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit deltaG, H651Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD2TIF224YGR083C
UniProt
Find proteins for P12754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilonI, J712Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD6TIF225YDR211WYD8142.12YD8142B.03
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaK, L304Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit gammaM, O [auth N]527Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD11TIF213YER025W
EC: 3.6.5.3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit betaN [auth O], P285Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI3TIF212YPL237W
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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: 10.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-85814-P

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-12-18
    Changes: Other