› 3o62

X-ray diffraction
3.22Å resolution

Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link

Released:
DOI: 10.2210/pdb3o62/pdb
PDB entry 3o62 coloured by chain, front view.
PDB entry 3o62 coloured by chain, side view.
PDB entry 3o62 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Consequences of cisplatin binding on nucleosome structure and dynamics.
Todd RC, Lippard SJ
Chem Biol 17 1334-43 (2010)
PMID: 21168769

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116638 (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: 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
Structure domains: Histone, subunit A
DNA (146-MER) Chain: I
Molecule details ›
Chain: I
Length: 146 nucleotides
Theoretical weight: 44.74 KDa
DNA (146-MER) Chain: J
Molecule details ›
Chain: J
Length: 146 nucleotides
Theoretical weight: 45.37 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 106.095Å b: 109.551Å c: 177.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.252 0.249 0.306
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Mitochondrial DNA damage and its consequences for mitochondrial gene expression.
Cline SD. (2012)
9 more

1 mention without citation

Consequences of cisplatin binding on nucleosome structure and dynamics.
Todd et al. (2010)