4qxb

X-ray diffraction
1.6Å resolution

crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG

Released:

Function and Biology Details

Reaction 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)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-157942 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific demethylase 2A Chains: A, C
Molecule details ›
Chains: A, C
Length: 329 amino acids
Theoretical weight: 39.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59997 (Residues: 36-364; Coverage: 28%)
Gene names: Fbl11, Fbxl11, Jhdm1a, Kdm2a, Kiaa1004
Sequence domains: Jumonji helical domain
Structure domains: Cupin
Lysine-specific demethylase 2A Chains: B, D
Molecule details ›
Chains: B, D
Length: 68 amino acids
Theoretical weight: 7.53 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59997 (Residues: 450-517; Coverage: 6%)
Gene names: Fbl11, Fbxl11, Jhdm1a, Kdm2a, Kiaa1004
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Histone H3.2 Chains: E, F
Molecule details ›
Chains: E, F
Length: 15 amino acids
Theoretical weight: 1.68 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: P84228 (Residues: 30-44; Coverage: 11%)
Gene names: H3-143, H3-53, H3-B, H3-F, H3.2, H3.2-221, H3.2-614, H3.2-615, H3.2-616, H3b, H3c13, H3c14, H3c15, H3c2, H3c3, H3c4, H3c6, H3c7, H3f, Hist1h3b, Hist1h3c, Hist1h3d, Hist1h3e, Hist1h3f, Hist2h3b, Hist2h3c1, Hist2h3c2, Hist2h3ca1, Hist2h3ca2

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 54.604Å b: 86.724Å c: 171.102Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.207
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided