PDBe 3av2

X-ray diffraction
2.8Å resolution

The human nucleosome structure containing the histone variant H3.3

Released:
Source organism: Homo sapiens
Primary publication:
Structures of human nucleosomes containing major histone H3 variants.
Acta Crystallogr. D Biol. Crystallogr. 67 578-83 (2011)
PMID: 21636898

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 H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 106 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H3.3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84243 (Residues: 1-136; Coverage: 100%)
Gene names: H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2B type 1-J Chains: D, H
Molecule details ›
Chains: D, H
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H2A type 1-B/E Chains: C, G
Molecule details ›
Chains: C, G
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Structure domains: Histone, subunit A
146-MER DNA Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 105.843Å b: 109.686Å c: 181.177Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.272
Expression system: Escherichia coli