7RUQ

Structure of the human GIGYF1-TNRC6C complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for GIGYF-TNRC6 complex assembly.

Sobti, M.Mead, B.J.Stewart, A.G.Igreja, C.Christie, M.

(2023) RNA 29: 724-734

  • DOI: https://doi.org/10.1261/rna.079596.123
  • Primary Citation of Related Structures:  
    7RUP, 7RUQ

  • PubMed Abstract: 

    The GIGYF proteins interact with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2-4EHP complex is recruited to its target transcripts remain unclear. Here, we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from the miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domains, thereby bridging 4EHP to Argonaute-miRNA complexes. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.


  • Organizational Affiliation

    Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GRB10-interacting GYF protein 1A,
B [auth C]
73Homo 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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trinucleotide repeat-containing gene 6C proteinC [auth D],
D [auth B]
16Homo sapiensMutation(s): 0 
Gene Names: TNRC6CKIAA1582
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCJ0 (Homo sapiens)
Explore Q9HCJ0 
Go to UniProtKB:  Q9HCJ0
PHAROS:  Q9HCJ0
GTEx:  ENSG00000078687 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCJ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSU
Query on CSU
A,
B [auth C]
L-PEPTIDE LINKINGC3 H7 N O5 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.918α = 90
b = 32.503β = 133.836
c = 69.578γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE160100608

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description