› 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 3o62 coloured by chain and viewed from the front.
PDB 3o62 coloured by chain and viewed from the side.
PDB 3o62 coloured by chain and viewed from the top.
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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (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

8 review citations

Molecular Epigenetics: Chemical Biology Tools Come of Age.
Bagert et al. (2021)
7 more

1 mention without citation

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