› 2wwu

X-ray diffraction
2.15Å resolution

Crystal structure of the catalytic domain of PHD finger protein 8

Released:
DOI: 10.2210/pdb2wwu/pdb
PDB entry 2wwu coloured by chain, front view.
PDB entry 2wwu coloured by chain, side view.
PDB entry 2wwu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase.
Yue WW, Hozjan V, Ge W, Loenarz C, Cooper CD, Schofield CJ, Kavanagh KL, Oppermann U, McDonough MA
FEBS Lett 584 825-30 (2010)
PMID: 20067792

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194030 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone lysine demethylase PHF8 Chain: A
Molecule details ›
Chain: A
Length: 371 amino acids
Theoretical weight: 42.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UPP1 (Residues: 115-483; Coverage: 35%)
Gene names: KIAA1111, PHF8, ZNF422
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 7 x SO4
Ligand ACT 5 x ACT
Ligand NI 1 x NI
Ligand BGC 2 x BGC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: I213
Unit cell:
a: 150.98Å b: 150.98Å c: 150.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Inhibition of 2-oxoglutarate dependent oxygenases.
Rose et al. (2011)
7 more

5 mentions without citation

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Black et al. (2012)
4 more