› 6r25

Electron Microscopy
4.61Å resolution

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3

Released:
DOI: 10.2210/pdb6r25/pdb
PDB entry 6r25 coloured by chain, front view.
PDB entry 6r25 coloured by chain, side view.
PDB entry 6r25 coloured by chain, top view.
Source organisms:
Primary publication:
A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A
Cell Rep 27 387-399.e7 (2019)
PMID: 30970244
Related structures: EMD-4710

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 tridecamer (preferred)
PDBe Complex ID:
PDB-CPX-120522 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
Lysine-specific histone demethylase 2 Chain: K
Molecule details ›
Chain: K
Length: 776 amino acids
Theoretical weight: 87.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NB78 (Residues: 51-822; Coverage: 94%)
Gene names: AOF1, C6orf193, KDM1B, LSD2
Sequence domains:
Cytokine-like nuclear factor N-PAC Chain: L
Molecule details ›
Chain: L
Length: 12 amino acids
Theoretical weight: 1.48 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q49A26 (Residues: 214-225; Coverage: 2%)
Gene names: GLYR1, HIBDL, NDF, NP60, NPAC
Histone H3.2 Chain: M
Molecule details ›
Chain: M
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 H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 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
Molecule details ›
Chains: 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
Molecule details ›
Chains: 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
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.61 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.14 KDa

Ligands and Environments

2 bound ligands:
Ligand FAD 1 x FAD
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.61Å
Relevant EMDB volumes: EMD-4710
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Histone Tail Conformations: A Fuzzy Affair with DNA.
Ghoneim et al. (2021)
11 other articles