PDBe 1f66

X-ray diffraction
2.6Å resolution

2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.51 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62806 (Residues: 1-103; Coverage: 100%)
Gene names: H4-12, H4-53, Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4, Hist2h4a, Hist4h4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2A.Z Chains: C, G
Molecule details ›
Chains: C, G
Length: 128 amino acids
Theoretical weight: 13.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C0S5 (Residues: 1-128; Coverage: 100%)
Gene names: H2AFZ, H2AZ
Sequence domains:
Structure domains: Histone, subunit A
PALINDROMIC 146 BASE PAIR DNA FRAGMENT Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.06 KDa

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 105.66Å b: 183.207Å c: 109.922Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.192 0.25
Expression system: Escherichia coli