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 1.1 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:  

  • 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 affec ...

    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

    Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas and CIBERER-ISCIII, Valencia, 46010, Spain. jllacer@ibv.csic.es.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. jllacer@ibv.csic.es.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit alpha
A, B
305Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCN3 (AAS2, TIF221)
Find proteins for P14741 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14741
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit beta
C, D
381Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD7 (TIF222)
Find proteins for P32502 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32502
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit gamma
E, F
578Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD1 (TIF223, TRA3)
Find proteins for P09032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P09032
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit delta
G, H
651Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD2 (TIF224)
Find proteins for P12754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P12754
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor eIF-2B subunit epsilon
I, J
712Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD6 (TIF225)
Find proteins for P32501 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32501
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit alpha
K, L
304Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUI2 (TIF211)
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20459
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit gamma
M, N
527Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD11 (TIF213)
Find proteins for P32481 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32481
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit beta
O, P
285Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUI3 (TIF212)
Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P09064
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
K, L
L-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 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Type: Data collection, Experimental preparation