› 4wu8

X-ray diffraction
2.45Å resolution

Structure of trPtNAP-NCP145

Released:
DOI: 10.2210/pdb4wu8/pdb
PDB entry 4wu8 coloured by chain, front view.
PDB entry 4wu8 coloured by chain, side view.
PDB entry 4wu8 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents.
Chua EY, Davey GE, Chin CF, Dröge P, Ang WH, Davey CA
OpenAccess logo Nucleic Acids Res 43 5284-96 (2015)
PMID: 25916851

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-118232 (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: 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:
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
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.75 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.74 KDa

Ligands and Environments

3 bound ligands:
Ligand CX3 2 x CX3
Ligand SO4 2 x SO4
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 106.41Å b: 109.63Å c: 183.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.214 0.263
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies.
Palermo et al. (2016)
5 other articles

1 mention without citation

Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents.
Chua et al. (2015)