› 2oq6

X-ray diffraction
2Å resolution

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9

Released:
DOI: 10.2210/pdb2oq6/pdb
PDB entry 2oq6 coloured by chain, front view.
PDB entry 2oq6 coloured by chain, side view.
PDB entry 2oq6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U
Nature 448 87-91 (2007)
PMID: 17589501

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130866 (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
UniProt:
  • Canonical: O75164 (Residues: 1-359; Coverage: 34%)
Gene names: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677
Sequence domains:
Structure domains: Cupin
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 890 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 8-15; Coverage: 6%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

3 bound ligands:
Ligand NI 2 x NI
Ligand ZN 2 x ZN
Ligand OGA 2 x OGA
2 modified residues:
Ligand M3L 2 x M3L
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21212
Unit cell:
a: 101.347Å b: 149.88Å c: 57.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.208
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

64 review citations

Molecular mechanisms and potential functions of histone demethylases.
Kooistra et al. (2012)
63 more

41 mentions without citation

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