› 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 entry 2fj7 coloured by chain, front view.
PDB entry 2fj7 coloured by chain, side view.
PDB entry 2fj7 coloured by chain, top view.
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:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115259 (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

Poly(dA:dT) tracts: major determinants of nucleosome organization.
Segal et al. (2009)
10 more

6 mentions without citation

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