7RUQ | pdb_00007ruq

Structure of the human GIGYF1-TNRC6C complex

• PDB DOI: https://doi.org/10.2210/pdb7RUQ/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-18 Released: 2022-08-24 
• Deposition Author(s): Sobti, M., Mead, B.J., Igreja, C., Stewart, A.G., Christie, M.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

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

• PubMed: 36854607 
• DOI: https://doi.org/10.1261/rna.079596.123
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, New South Wales 2052, Australia.
School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia.
Department of Integrative Evolutionary Biology, Max Planck Institute for Biology, D-72076 Tübingen, Germany [e-mail] [e-mail].
Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.6 kDa 
• Atom Count: 1,210 
• Modeled Residue Count: 142 
• Deposited Residue Count: 178 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRB10-interacting GYF protein 1	A, B [auth C]	73	Homo sapiens	Mutation(s): 0  Gene Names: GIGYF1, CDS2, PERQ1, PP3360
UniProt & NIH Common Fund Data Resources
Find proteins for O75420 (Homo sapiens) Explore O75420  Go to UniProtKB:  O75420
PHAROS:  O75420 GTEx:  ENSG00000146830

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trinucleotide repeat-containing gene 6C protein	C [auth D], D [auth B]	16	Homo sapiens	Mutation(s): 0  Gene Names: TNRC6C, KIAA1582
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCJ0 (Homo sapiens) Explore Q9HCJ0  Go to UniProtKB:  Q9HCJ0
PHAROS:  Q9HCJ0 GTEx:  ENSG00000078687

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSU	A, B [auth C]	L-PEPTIDE LINKING	C3 H7 N O5 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.918	α = 90
b = 32.503	β = 133.836
c = 69.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Sobti, M., Mead, B.J., Igreja, C., Stewart, A.G., Christie, M.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE160100608

Revision History  

• 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