› 6r1t

Electron Microscopy
3.7Å resolution

Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome

Released:
DOI: 10.2210/pdb6r1t/pdb
PDB entry 6r1t coloured by chain, front view.
PDB entry 6r1t coloured by chain, side view.
PDB entry 6r1t coloured by chain, top view.
Source organism: Xenopus laevis
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-4704

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238547 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 99 amino acids
Theoretical weight: 11.63 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 38-136; Coverage: 73%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 87 amino acids
Theoretical weight: 9.99 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 17-103; Coverage: 85%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 111 amino acids
Theoretical weight: 12.18 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 11-121; Coverage: 85%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 96 amino acids
Theoretical weight: 10.79 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 30-125; Coverage: 76%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4704
Expression system: Escherichia coli

Quick links

Citations

1 review citation

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

2 mentions without citation

Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1.
Gaullier et al. (2020)
1 more