› 4hsu

X-ray diffraction
1.99Å resolution

Crystal structure of LSD2-NPAC with H3(1-26)in space group P21

Released:
DOI: 10.2210/pdb4hsu/pdb
PDB entry 4hsu coloured by chain, front view.
PDB entry 4hsu coloured by chain, side view.
PDB entry 4hsu coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into substrate recognition by histone demethylase LSD2/KDM1b.
Chen F, Yang H, Dong Z, Fang J, Wang P, Zhu T, Gong W, Fang R, Shi YG, Li Z, Xu Y
Cell Res 23 306-9 (2013)
PMID: 23357850

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + acceptor + H(2)O = a [histone H3]-N(6)-methyl-L-lysine(4) + formaldehyde + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-175408 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific histone demethylase 2 Chain: A
Molecule details ›
Chain: A
Length: 776 amino acids
Theoretical weight: 87.05 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8NB78 (Residues: 51-822; Coverage: 94%)
Gene names: AOF1, C6orf193, KDM1B, LSD2
Sequence domains:
Cytokine-like nuclear factor N-PAC Chain: B
Molecule details ›
Chain: B
Length: 124 amino acids
Theoretical weight: 13.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q49A26 (Residues: 152-268; Coverage: 21%)
Gene names: GLYR1, HIBDL, NDF, NP60, NPAC
Histone H3 Chain: C
Molecule details ›
Chain: C
Length: 30 amino acids
Theoretical weight: 3.18 KDa
Source organism: Xenopus laevis
Expression system: Not provided
UniProt:
  • Canonical: Q92133 (Residues: 2-31; Coverage: 22%)
Gene names: H3l, Hist1h3f, h3, h3.2a, h3c8, h3c8.S, h3r, hist1h3g, hist1h3g.L, hist2h3, hist2h3c

Ligands and Environments

2 bound ligands:
Ligand FAD 1 x FAD
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 62.754Å b: 89.481Å c: 88.349Å
α: 90° β: 102.89° γ: 90°
R-values:
R R work R free
0.2 0.199 0.232
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli
  • Not provided

Quick links

Citations

17 review citations

Histone lysine demethylases as targets for anticancer therapy.
Højfeldt et al. (2013)
16 more

6 mentions without citation

KDM1 class flavin-dependent protein lysine demethylases.
Burg et al. (2015)
5 more