6f6d

X-ray diffraction
1.82Å resolution

The catalytic domain of KDM6B in complex with H3(17-33)K18IA21M peptide

Released:
Source organism: Homo sapiens
Primary publication:
Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity.
Biochemistry 57 585-592 (2018)
PMID: 29220567

Function and Biology Details

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(27) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(27) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase 6B Chain: A
Molecule details ›
Chain: A
Length: 510 amino acids
Theoretical weight: 58.05 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O15054 (Residues: 1141-1643; Coverage: 31%)
Gene names: JMJD3, KDM6B, KIAA0346
Sequence domains: JmjC domain, hydroxylase
Structure domains:
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 17 amino acids
Theoretical weight: 1.8 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 18-34; Coverage: 13%)
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

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P41212
Unit cell:
a: 68.48Å b: 68.48Å c: 230Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.165 0.214
Expression systems:
  • Spodoptera frugiperda
  • Not provided