3kv4

X-ray diffraction
2.19Å resolution

Structure of PHF8 in complex with histone H3

Released:

Function and Biology Details

Reactions catalysed:
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(9) + succinate + formaldehyde + CO(2)
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-180080 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone lysine demethylase PHF8 Chain: A
Molecule details ›
Chain: A
Length: 447 amino acids
Theoretical weight: 51.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UPP1 (Residues: 37-483; Coverage: 42%)
Gene names: KIAA1111, PHF8, ZNF422
Sequence domains:
Structure domains:
Histone H3.3C Chain: B
Molecule details ›
Chain: B
Length: 24 amino acids
Theoretical weight: 2.63 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q6NXT2 (Residues: 2-25; Coverage: 18%)
Gene names: H3-5, H3F3C

Ligands and Environments

2 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43212
Unit cell:
a: 73.5Å b: 73.5Å c: 210.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.255
Expression systems:
  • Escherichia coli
  • Not provided