› 2fj7

X-ray diffraction
3.2Å resolution

Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element

Released:
DOI: 10.2210/pdb2fj7/pdb
PDB 2fj7 coloured by chain and viewed from the front.
PDB 2fj7 coloured by chain and viewed from the side.
PDB 2fj7 coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure.
Bao Y, White CL, Luger K
J. Mol. Biol. 361 617-24 (2006)
PMID: 16860337

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

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: 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
147 bp DNA containing 16 bp poly dA element Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
147 bp DNA containing 16 bp poly dT element Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.35 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 104.918Å b: 109.598Å c: 177.969Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.28 0.28 0.35
Expression system: Escherichia coli

Quick links

Citations

11 review citations

The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.
Barnes et al. (2021)
10 more

6 mentions without citation

Electrostatic interactions between arginines and the minor groove in the nucleosome.
West et al. (2010)
5 more