› 3b6f

X-ray diffraction
3.45Å resolution

Nucleosome core particle treated with cisplatin

Released:
DOI: 10.2210/pdb3b6f/pdb
PDB entry 3b6f coloured by chain, front view.
PDB entry 3b6f coloured by chain, side view.
PDB entry 3b6f coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Site selectivity of platinum anticancer therapeutics.
Wu B, Dröge P, Davey CA
Nat Chem Biol 4 110-2 (2008)
PMID: 18157123

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116086 (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: 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
Structure domains: Histone, subunit A
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
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 128 amino acids
Theoretical weight: 13.91 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
147-MER DNA Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
147-MER DNA Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.36 KDa

Ligands and Environments

1 bound ligand:
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.327Å b: 109.38Å c: 180.585Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.331 0.33 0.402
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Inhibition of transcription by platinum antitumor compounds.
Todd et al. (2009)
10 more

5 mentions without citation

Nucleosome structural studies.
Tan et al. (2011)
4 more