› 7yyj

X-ray diffraction
2.1Å resolution

Tetragonal crystal structure of YTHDF1 YTH domain (544AVV546 mutant)

Released:
DOI: 10.2210/pdb7yyj/pdb
PDB entry 7yyj coloured by chain, front view.
PDB entry 7yyj coloured by chain, side view.
PDB entry 7yyj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains.
Cazzanelli G, Dalle Vedove A, Spagnolli G, Terruzzi L, Colasurdo E, Boldrini A, Patsilinakos A, Sturlese M, Grottesi A, Biasini E, Provenzani A, Quattrone A, Lolli G
J Chem Inf Model (2024)
PMID: 38417111

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189836 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain-containing family protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 200 amino acids
Theoretical weight: 23.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BYJ9 (Residues: 361-559; Coverage: 36%)
  • Best match: Q9BYJ9-2 (Residues: 176-197)
Gene names: C20orf21, YTHDF1
Sequence domains: YT521-B-like domain

Ligands and Environments

2 bound ligands:
Ligand EDO 4 x EDO
Ligand SCN 2 x SCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 11.2C
Spacegroup: P43212
Unit cell:
a: 120.841Å b: 120.841Å c: 79.636Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.197 0.229
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

The three YTHDF paralogs and VIRMA are strong cross-histotype tumor driver candidates among m<sup>6</sup>A core genes.
Destefanis et al. (2024)