› 6vyp

X-ray diffraction
4.99Å resolution

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

Released:
DOI: 10.2210/pdb6vyp/pdb
PDB entry 6vyp coloured by chain, front view.
PDB entry 6vyp coloured by chain, side view.
PDB entry 6vyp coloured by chain, top view.
Source organisms:
Primary publication:
Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate.
Kim SA, Zhu J, Yennawar N, Eek P, Tan S
Mol Cell 78 903-914.e4 (2020)
PMID: 32396821

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 tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-120789 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.2 Chains: A, E, a, e
Molecule details ›
Chains: A, E, a, e
Length: 135 amino acids
Theoretical weight: 15.31 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F, b, f
Molecule details ›
Chains: B, F, b, f
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G, c, g
Molecule details ›
Chains: C, G, c, g
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H, d, h
Molecule details ›
Chains: D, H, d, h
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Lysine-specific histone demethylase 1A Chains: K, M, k, m
Molecule details ›
Chains: K, M, k, m
Length: 684 amino acids
Theoretical weight: 75.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 171-852; Coverage: 80%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
REST corepressor 1 Chains: L, N, l, n
Molecule details ›
Chains: L, N, l, n
Length: 157 amino acids
Theoretical weight: 17.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKL0 (Residues: 289-443; Coverage: 32%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains:
DNA (191-MER) Chains: I, i
Molecule details ›
Chains: I, i
Length: 191 nucleotides
Theoretical weight: 58.69 KDa
DNA (191-MER) Chains: J, j
Molecule details ›
Chains: J, j
Length: 191 nucleotides
Theoretical weight: 59.25 KDa

Ligands and Environments

1 bound ligand:
Ligand FAD 4 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 103.771Å b: 335.77Å c: 174.633Å
α: 90° β: 91.07° γ: 90°
R-values:
R R work R free
0.231 0.229 0.277
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
6 more

5 mentions without citation

Distinct biochemical properties of the class I histone deacetylase complexes.
Lee et al. (2022)
4 more