› 1eqz

X-ray diffraction
2.5Å resolution

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

Released:
DOI: 10.2210/pdb1eqz/pdb
PDB entry 1eqz coloured by chain, front view.
PDB entry 1eqz coloured by chain, side view.
PDB entry 1eqz coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Asymmetries in the nucleosome core particle at 2.5 A resolution.
Harp JM, Hanson BL, Timm DE, Bunick GJ
Acta Crystallogr D Biol Crystallogr 56 1513-34 (2000)
PMID: 11092917

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-113763 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H2A-IV Chains: A, E
Molecule details ›
Chains: A, E
Length: 129 amino acids
Theoretical weight: 13.97 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P02263 (Residues: 1-129; Coverage: 100%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 7 Chains: B, F
Molecule details ›
Chains: B, F
Length: 126 amino acids
Theoretical weight: 13.95 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P0C1H5 (Residues: 1-126; Coverage: 100%)
Gene name: H2B-VII
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H3.2 Chains: C, G
Molecule details ›
Chains: C, G
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P84229 (Residues: 1-136; Coverage: 100%)
Gene names: H3-I, H3-II, H3-III, H3-IV, H3-V, H3-VI, H3-VII, H3-VIII
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: D, H
Molecule details ›
Chains: D, H
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P62801 (Residues: 1-103; Coverage: 100%)
Gene names: H4-I, H4-II, H4-III, H4-IV, H4-V, H4-VI, H4-VII
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
146 NUCLEOTIDES LONG DNA Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

4 bound ligands:
Ligand K 7 x K
Ligand MN 15 x MN
Ligand CL 2 x CL
Ligand CAC 1 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 105.28Å b: 109.71Å c: 181.12Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.219 0.282

Quick links

Citations

27 review citations

The nucleosome: from genomic organization to genomic regulation.
Khorasanizadeh S. (2004)
26 more

31 mentions without citation

Histone structure and nucleosome stability.
Mariño-Ramírez et al. (2005)
30 more