› 3rej

X-ray diffraction
2.55Å resolution

2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b)

Released:
DOI: 10.2210/pdb3rej/pdb
PDB 3rej coloured by chain and viewed from the front.
PDB 3rej coloured by chain and viewed from the side.
PDB 3rej coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation.
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA
Nucleic Acids Res. 39 8200-12 (2011)
PMID: 21724603

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
1 distinct DNA molecule
Macromolecules (5 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: 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) Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

2 bound ligands:
Ligand MN 13 x MN
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.067Å b: 109.374Å c: 176.465Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.262
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Frontiers of metal-coordinating drug design.
Palermo et al. (2021)
4 more

2 mentions without citation

Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation.
Wu et al. (2011)
1 more