› 8hcu

X-ray diffraction
2.2Å resolution

Crystal structure of BCOR/PCGF1/KDM2B complex

Released:
DOI: 10.2210/pdb8hcu/pdb
PDB entry 8hcu coloured by chain, front view.
PDB entry 8hcu coloured by chain, side view.
PDB entry 8hcu coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Shen F, Chen R, Xu J, Liu J

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-240929 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific demethylase 2B Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 26.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NHM5 (Residues: 1103-1336; Coverage: 18%)
Gene names: CXXC2, FBL10, FBXL10, JHDM1B, KDM2B, NDY1, PCCX2
Polycomb group RING finger protein 1 Chain: B
Molecule details ›
Chain: B
Length: 105 amino acids
Theoretical weight: 12.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BSM1 (Residues: 151-255; Coverage: 41%)
Gene names: NSPC1, PCGF1, RNF68
Sequence domains: RAWUL domain RING finger- and WD40-associated ubiquitin-like
BCL-6 corepressor Chain: C
Molecule details ›
Chain: C
Length: 142 amino acids
Theoretical weight: 16.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6W2J9 (Residues: 1607-1748; Coverage: 8%)
Gene names: BCOR, KIAA1575
Sequence domains: BCORL-PCGF1-binding domain

Ligands and Environments

1 bound ligand:
Ligand ACY 2 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P43212
Unit cell:
a: 67.291Å b: 67.291Å c: 252.035Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.238
Expression system: Escherichia coli BL21(DE3)

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