7RUP

Structure of the human GIGYF2-TNRC6A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 273Homo sapiensMutation(s): 0 
Gene Names: GIGYF2KIAA0642PERQ2TNRC15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6Y7W6 (Homo sapiens)
Explore Q6Y7W6 
Go to UniProtKB:  Q6Y7W6
PHAROS:  Q6Y7W6
GTEx:  ENSG00000204120 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Y7W6
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trinucleotide repeat-containing gene 6A protein16Homo sapiensMutation(s): 0 
Gene Names: TNRC6ACAGH26KIAA1460TNRC6
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NDV7 (Homo sapiens)
Explore Q8NDV7 
Go to UniProtKB:  Q8NDV7
PHAROS:  Q8NDV7
GTEx:  ENSG00000090905 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NDV7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.779α = 90
b = 38.319β = 90
c = 62.064γ = 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
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1159347
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1146403

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
  • Version 1.4: 2023-11-15
    Changes: Data collection