7RUP | pdb_00007rup

Structure of the human GIGYF2-TNRC6A complex

PDB DOI: https://doi.org/10.2210/pdb7RUP/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: 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), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free:
0.177 (Depositor), 0.177 (DCC)
R-Value Work:
0.152 (Depositor), 0.154 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 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

PubMed: 36854607 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 10.03 kDa
Atom Count: 697
Modeled Residue Count: 72
Deposited Residue Count: 89
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRB10-interacting GYF protein 2	A	73	Homo sapiens	Mutation(s): 0 Gene Names: GIGYF2, KIAA0642, PERQ2, TNRC15
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6Y7W6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trinucleotide repeat-containing gene 6A protein	B	16	Homo sapiens	Mutation(s): 0 Gene Names: TNRC6A, CAGH26, KIAA1460, TNRC6
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NDV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.177 (Depositor), 0.177 (DCC)
R-Value Work: 0.152 (Depositor), 0.154 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.779	α = 90
b = 38.319	β = 90
c = 62.064	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE160100608
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1159347
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1146403