X-ray diffraction
3Å resolution

Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1.


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:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 734 amino acids
Theoretical weight: 81.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: O60341 (Residues: 123-369, 370-852; Coverage: 86%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
Structure domains:
REST corepressor 1 Chain: B
Molecule details ›
Chain: B
Length: 133 amino acids
Theoretical weight: 15.32 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: Q9UKL0 (Residues: 311-443; Coverage: 27%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains: Myb-like DNA-binding domain
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 16 amino acids
Theoretical weight: 1.66 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: P68431 (Residues: 2-17; Coverage: 12%)
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

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: I222
Unit cell:
a: 119.69Å b: 181.21Å c: 233.45Å
α: 90° β: 90° γ: 90°
R R work R free
0.213 0.212 0.252
Expression systems:
  • Escherichia coli
  • Not provided