› 3kuy

X-ray diffraction
2.9Å resolution

DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent

Released:
DOI: 10.2210/pdb3kuy/pdb
PDB 3kuy coloured by chain and viewed from the front.
PDB 3kuy coloured by chain and viewed from the side.
PDB 3kuy coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent.
Davey GE, Wu B, Dong Y, Surana U, Davey CA
Nucleic Acids Res. 38 2081-8 (2010)
PMID: 20026584

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: 119 amino acids
Theoretical weight: 12.94 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-120; Coverage: 92%)
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

2 bound ligands:
Ligand MN 1 x MN
Ligand ATV 2 x ATV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 106.161Å b: 109.588Å c: 182.413Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.238 0.286
Expression system: Escherichia coli

Quick links

Citations

25 citation in other articles

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence.
Vasudevan et al. (2010)
24 more

4 mentions without citation

Nucleosome structural studies.
Tan et al. (2011)
3 more