6QG6

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41467-019-10606-1
  • Primary Citation of Related Structures:  
    6QG0, 6QG1, 6QG2, 6QG3, 6QG5, 6QG6

  • 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. 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alpha
A, B
305Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCN3AAS2TIF221YKR026C
UniProt
Find proteins for P14741 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14741 
Go to UniProtKB:  P14741
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14741
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit beta
C, D
381Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD7TIF222YLR291CL8003.17
UniProt
Find proteins for P32502 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32502 
Go to UniProtKB:  P32502
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32502
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit gamma
E, F
578Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD1TIF223TRA3YOR260W
UniProt
Find proteins for P09032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09032 
Go to UniProtKB:  P09032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09032
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit delta
G, H
651Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD2TIF224YGR083C
UniProt
Find proteins for P12754 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P12754 
Go to UniProtKB:  P12754
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12754
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit epsilon
I, J
712Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD6TIF225YDR211WYD8142.12YD8142B.03
UniProt
Find proteins for P32501 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32501 
Go to UniProtKB:  P32501
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32501
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alpha
K, L
304Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20459 
Go to UniProtKB:  P20459
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20459
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit gammaM,
O [auth N]
527Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GCD11TIF213YER025W
EC: 3.6.5.3
UniProt
Find proteins for P32481 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32481 
Go to UniProtKB:  P32481
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32481
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit betaN [auth O],
P
285Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUI3TIF212YPL237W
UniProt
Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09064 
Go to UniProtKB:  P09064
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09064
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
K, L
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Refinement description, Structure summary