› 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 entry 3kuy coloured by chain, front view.
PDB entry 3kuy coloured by chain, side view.
PDB entry 3kuy coloured by chain, top view.
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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116507 (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

28 citation in other articles

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

4 mentions without citation

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