› 8q1j

X-ray diffraction
2.87Å resolution

LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3

Released:
DOI: 10.2210/pdb8q1j/pdb
PDB entry 8q1j coloured by chain, front view.
PDB entry 8q1j coloured by chain, side view.
PDB entry 8q1j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.
Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA
Nat Chem Biol (2024)
PMID: 38965385

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:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-244373 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 730 amino acids
Theoretical weight: 81.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O60341 (Residues: 123-852; Coverage: 86%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
REST corepressor 1 Chain: B
Molecule details ›
Chain: B
Length: 178 amino acids
Theoretical weight: 20.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9UKL0 (Residues: 308-485; Coverage: 37%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains:
Histone H3.3C Chain: C
Molecule details ›
Chain: C
Length: 21 amino acids
Theoretical weight: 2.3 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q6NXT2 (Residues: 2-22; Coverage: 16%)
Gene names: H3-5, H3F3C

Ligands and Environments

1 bound ligand:
Ligand FAD 1 x FAD
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: I222
Unit cell:
a: 118.598Å b: 180.153Å c: 232.678Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.24 0.272
Expression systems:
  • Escherichia coli BL21
  • Not provided

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