5NVK

Crystal structure of the human 4EHP-GIGYF1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

GIGYF1/2 proteins use auxiliary sequences to selectively bind to 4EHP and repress target mRNA expression.

Peter, D.Weber, R.Sandmeir, F.Wohlbold, L.Helms, S.Bawankar, P.Valkov, E.Igreja, C.Izaurralde, E.

(2017) Genes Dev 31: 1147-1161

  • DOI: https://doi.org/10.1101/gad.299420.117
  • Primary Citation of Related Structures:  
    5NVK, 5NVL, 5NVM, 5NVN

  • PubMed Abstract: 

    The eIF4E homologous protein (4EHP) is thought to repress translation by competing with eIF4E for binding to the 5' cap structure of specific mRNAs to which it is recruited through interactions with various proteins, including the GRB10-interacting GYF (glycine-tyrosine-phenylalanine domain) proteins 1 and 2 (GIGYF1/2). Despite its similarity to eIF4E, 4EHP does not interact with eIF4G and therefore fails to initiate translation. In contrast to eIF4G, GIGYF1/2 bind selectively to 4EHP but not eIF4E. Here, we present crystal structures of the 4EHP-binding regions of GIGYF1 and GIGYF2 in complex with 4EHP, which reveal the molecular basis for the selectivity of the GIGYF1/2 proteins for 4EHP. Complementation assays in a GIGYF1/2-null cell line using structure-based mutants indicate that 4EHP requires interactions with GIGYF1/2 to down-regulate target mRNA expression. Our studies provide structural insights into the assembly of 4EHP-GIGYF1/2 repressor complexes and reveal that rather than merely facilitating 4EHP recruitment to transcripts, GIGYF1/2 proteins are required for repressive activity.


  • Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E type 2
A, C, E, G
189Homo sapiensMutation(s): 0 
Gene Names: EIF4E2EIF4EL3
UniProt & NIH Common Fund Data Resources
Find proteins for O60573 (Homo sapiens)
Explore O60573 
Go to UniProtKB:  O60573
PHAROS:  O60573
GTEx:  ENSG00000135930 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60573
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GRB10-interacting GYF protein 1
B, D, F, H
75Homo sapiensMutation(s): 0 
Gene Names: GIGYF1CDS2PERQ1PP3360
UniProt & NIH Common Fund Data Resources
Find proteins for O75420 (Homo sapiens)
Explore O75420 
Go to UniProtKB:  O75420
PHAROS:  O75420
GTEx:  ENSG00000146830 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75420
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.32α = 90
b = 135.32β = 90
c = 60.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description