› 4gur

X-ray diffraction
2.51Å resolution

Crystal structure of LSD2-NPAC with H3 in space group P21

Released:
DOI: 10.2210/pdb4gur/pdb
PDB entry 4gur coloured by chain, front view.
PDB entry 4gur coloured by chain, side view.
PDB entry 4gur coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation.
Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, Simon MD, Zhou Q, Li J, Marynick MP, Li X, Lu H, Kaiser UB, Kingston RE, Xu Y, Shi YG
Mol Cell 49 558-70 (2013)
PMID: 23260659

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-160859 (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 H3.3 Chain: C
Molecule details ›
Chain: C
Length: 21 amino acids
Theoretical weight: 2.26 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 2-22; Coverage: 15%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

3 bound ligands:
Ligand FAD 1 x FAD
Ligand GOL 1 x GOL
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: 62.243Å b: 89.033Å c: 88.783Å
α: 90° β: 103.3° γ: 90°
R-values:
R R work R free
0.189 0.188 0.204
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

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

2 mentions without citation

Touch, act and go: landing and operating on nucleosomes.
Speranzini et al. (2016)
1 more