› 5jh5

X-ray diffraction
2.55Å resolution

Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

Released:
DOI: 10.2210/pdb5jh5/pdb
PDB entry 5jh5 coloured by chain, front view.
PDB entry 5jh5 coloured by chain, side view.
PDB entry 5jh5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.
Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, Artigas JA, Lee OJ, Demeler B, Hart PJ, Bardwell VJ, Kim CA
Structure 24 1795-1801 (2016)
PMID: 27568929

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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-159040 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Lysine-specific demethylase 2B Chain: A
Molecule details ›
Chain: A
Length: 281 amino acids
Theoretical weight: 32.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NHM5 (Residues: 1059-1336; Coverage: 21%)
  • Best match: Q8NHM5-3 (Residues: 1047-1326)
Gene names: CXXC2, FBL10, FBXL10, JHDM1B, KDM2B, NDY1, PCCX2
Sequence domains: F-box-like
S-phase kinase-associated protein 1 Chain: B
Molecule details ›
Chain: B
Length: 162 amino acids
Theoretical weight: 18.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63208 (Residues: 2-163; Coverage: 99%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Structure domains: Potassium Channel Kv1.1; Chain A
Polycomb group RING finger protein 1 Chain: C
Molecule details ›
Chain: C
Length: 109 amino acids
Theoretical weight: 13.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BSM1 (Residues: 150-255; Coverage: 41%)
Gene names: NSPC1, PCGF1, RNF68
Sequence domains: RAWUL domain RING finger- and WD40-associated ubiquitin-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
BCL-6 corepressor-like protein 1 Chain: D
Molecule details ›
Chain: D
Length: 122 amino acids
Theoretical weight: 14.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H9F3 (Residues: 1668-1785; Coverage: 7%)
Gene name: BCORL1
Sequence domains: BCORL-PCGF1-binding domain

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 17 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 70.049Å b: 73.796Å c: 123.014Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.206 0.257
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Molecular architecture of polycomb repressive complexes.
Chittock et al. (2017)
12 more

4 mentions without citation

KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.
Wong et al. (2016)
3 more