› 5dnn

X-ray diffraction
2.8Å resolution

Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes

Released:
DOI: 10.2210/pdb5dnn/pdb
PDB entry 5dnn coloured by chain, front view.
PDB entry 5dnn coloured by chain, side view.
PDB entry 5dnn coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Allosteric cross-talk in chromatin can mediate drug-drug synergy.
Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R, Rothlisberger U, Dyson PJ, Davey CA
Nat Commun 8 14860 (2017)
PMID: 28358030

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-118579 (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
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

4 bound ligands:
Ligand AUF 2 x AUF
Ligand SO4 3 x SO4
Ligand MG 1 x MG
Ligand RAX 2 x RAX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 106.726Å b: 109.948Å c: 182.041Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.215 0.236
Expression system: Escherichia coli

Quick links

Citations

9 review citations

The development of anticancer ruthenium(ii) complexes: from single molecule compounds to nanomaterials.
Zeng et al. (2017)
8 more

1 mention without citation

Allosteric cross-talk in chromatin can mediate drug-drug synergy.
Adhireksan et al. (2017)