X-ray diffraction
1.9Å resolution

Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide


Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 5A Chain: A
Molecule details ›
Chain: A
Length: 52 amino acids
Theoretical weight: 5.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: P29375 (Residues: 1609-1659; Coverage: 3%)
Gene names: JARID1A, KDM5A, RBBP2, RBP2
Histone H3 Chain: B
Molecule details ›
Chain: B
Length: 9 amino acids
Theoretical weight: 1.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: Q92133 (Residues: 2-10; Coverage: 7%)
Gene names: H3l, h3c8, h3c8.S, hist1h3g

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I41
Unit cell:
a: 49.95Å b: 49.95Å c: 86.45Å
α: 90° β: 90° γ: 90°
R R work R free
0.229 0.208 0.225
Expression systems:
  • Escherichia coli
  • Not provided