› 4v2w

X-ray diffraction
1.81Å resolution

JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)

Released:
DOI: 10.2210/pdb4v2w/pdb
PDB entry 4v2w coloured by chain, front view.
PDB entry 4v2w coloured by chain, side view.
PDB entry 4v2w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Studies on the catalytic domains of multiple JmjC oxygenases using peptide substrates.
Williams ST, Walport LJ, Hopkinson RJ, Madden SK, Chowdhury R, Schofield CJ, Kawamura A
Epigenetics 9 1596-603 (2014)
PMID: 25625844

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-130874 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 4A Chains: A, B
Molecule details ›
Chains: A, B
Length: 381 amino acids
Theoretical weight: 44.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin
Histone H3.1t Chain: C
Molecule details ›
Chain: C
Length: 20 amino acids
Theoretical weight: 2.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q16695 (Residues: 17-36; Coverage: 15%)
Gene names: H3-4, H3FT, HIST3H3

Ligands and Environments

5 bound ligands:
Ligand NI 2 x NI
Ligand ZN 2 x ZN
Ligand CL 2 x CL
Ligand OGA 2 x OGA
Ligand GOL 1 x GOL
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21212
Unit cell:
a: 100.711Å b: 149.74Å c: 57.508Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
15 more

2 mentions without citation

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage.
Gray et al. (2015)
1 more