› 6we8

X-ray diffraction
1.18Å resolution

YTH domain of human YTHDC1

Released:
DOI: 10.2210/pdb6we8/pdb
PDB entry 6we8 coloured by chain, front view.
PDB entry 6we8 coloured by chain, side view.
PDB entry 6we8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X
OpenAccess logo Nucleic Acids Res 48 10329-10341 (2020)
PMID: 32663306

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-188634 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain-containing protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 166 amino acids
Theoretical weight: 18.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96MU7 (Residues: 345-509; Coverage: 23%)
Gene names: KIAA1966, YT521, YTHDC1
Sequence domains: YT521-B-like domain

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand EDO 8 x EDO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 39.914Å b: 103.96Å c: 42.201Å
α: 90° β: 104.869° γ: 90°
R-values:
R R work R free
0.166 0.166 0.195
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
6 more

1 mention without citation

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
Woodcock et al. (2020)