› 5afw

X-ray diffraction
1.6Å resolution

Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation

Released:
DOI: 10.2210/pdb5afw/pdb
PDB entry 5afw coloured by chain, front view.
PDB entry 5afw coloured by chain, side view.
PDB entry 5afw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation.
Metzger E, Willmann D, McMillan J, Forne I, Metzger P, Gerhardt S, Petroll K, von Maessenhausen A, Urban S, Schott AK, Espejo A, Eberlin A, Wohlwend D, Schüle KM, Schleicher M, Perner S, Bedford MT, Jung M, Dengjel J, Flaig R, Imhof A, Einsle O, Schüle R
Nat Struct Mol Biol 23 132-9 (2016)
PMID: 26751641

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
(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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127041 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromodomain-helicase-DNA-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 174 amino acids
Theoretical weight: 20.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O14646 (Residues: 270-443; Coverage: 10%)
Gene name: CHD1
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Lysine-specific histone demethylase 1A Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 108-119; Coverage: 1%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1

Ligands and Environments

2 bound ligands:
Ligand EDO 9 x EDO
Ligand CL 3 x CL
1 modified residue:
Ligand MLY 1 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 110.296Å b: 44.445Å c: 46.194Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.209 0.227
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy.
Morera et al. (2016)
14 more

3 mentions without citation

Potential Role of Antioxidant and Anti-Inflammatory Therapies to Prevent Severe SARS-Cov-2 Complications.
Fratta Pasini et al. (2021)
2 more