9F79 | pdb_00009f79

Crystal structure of the S. cerevisiae eIF2beta N-terminal tail bound to the C-terminal domain of eIF5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.228 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

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

Molecular basis for the interactions of eIF2 beta with eIF5, eIF2B, and 5MP1 and their regulation by CK2.

Wagner, P.A.Song, M.Doran, P.Seker, A.Ficner, R.Kuhle, B.Marintchev, A.

(2025) RNA 31: 1419-1435

  • DOI: https://doi.org/10.1261/rna.080652.125
  • Primary Citation of Related Structures:  
    9F79

  • PubMed Abstract: 

    The heterotrimeric GTPase eukaryotic translation initiation factor 2 (eIF2) delivers the initiator Met-tRNAi to the ribosomal translation preinitiation complex (PIC). eIF2β has three lysine-rich repeats (K-boxes), important for binding to the GTPase-activating protein eIF5, the guanine nucleotide exchange factor eIF2B, and the regulator eIF5-mimic protein (5MP). Here, we combine X-ray crystallography with NMR to understand the molecular basis and dynamics of these interactions. The crystal structure of yeast eIF5-CTD in complex with eIF2β K-box 3 reveals an extended binding site on eIF2β, far beyond the K-box. We show that eIF2β contains three distinct binding sites, centered on each of the K-boxes, and that human eIF5, eIF2Bε, and 5MP1 can bind to all three sites. Our results reveal how eIF2B speeds up the dissociation of eIF5 from eIF2-GDP to promote nucleotide exchange; and how 5MP1 can destabilize eIF5 binding to eIF2 and the PIC, to promote stringent start codon selection. All these affinities are increased by CK2 phosphomimetic mutations, highlighting the role of CK2 in both remodeling and stabilizing the translation apparatus.


  • Organizational Affiliation
    • Boston University Chobanian & Avedisian School of Medicine.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5
A, B
210Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF5YPR041WYP3085.05
UniProt
Find proteins for P38431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38431 
Go to UniProtKB:  P38431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38431
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit beta73Saccharomyces 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.228 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.18α = 90
b = 74.18β = 90
c = 224.42γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references