› 1f66

X-ray diffraction
2.6Å resolution

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

Released:
DOI: 10.2210/pdb1f66/pdb
PDB 1f66 coloured by chain and viewed from the front.
PDB 1f66 coloured by chain and viewed from the side.
PDB 1f66 coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
Suto RK, Clarkson MJ, Tremethick DJ, Luger K
Nat. Struct. Biol. 7 1121-4 (2000)
PMID: 11101893

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

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%)
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, H4c1, H4c11, H4c12, H4c14, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4f16, Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4, Hist2h4a, Hist4h4
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, H2AZ1
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%)
Structure domains: Histone, subunit A
PALINDROMIC 146 BASE PAIR DNA FRAGMENT Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

1 bound ligand:
Ligand MN 15 x MN
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

Quick links

Citations

111 review citations

The roles of histone variants in fine-tuning chromatin organization and function.
Martire et al. (2020)
110 more

21 mentions without citation

Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome.
Soshnev et al. (2016)
20 more