PDBe 5kdm

X-ray diffraction
3.5Å resolution

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Histone H3.3 Chain: A
Molecule details ›
Chain: A
Length: 135 amino acids
Theoretical weight: 15.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P84243 (Residues: 2-136; Coverage: 99%)
Gene names: H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Structure domains: Histone, subunit A
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
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
Death domain-associated protein 6 Chain: C
Molecule details ›
Chain: C
Length: 212 amino acids
Theoretical weight: 24.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UER7 (Residues: 178-389; Coverage: 29%)
Gene names: BING2, DAP6, DAXX
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Major tegument protein Chain: D
Molecule details ›
Chain: D
Length: 219 amino acids
Theoretical weight: 23.41 KDa
Source organism: Epstein-barr virus strain ag876
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1HVJ0 (Residues: 381-599; Coverage: 17%)
Gene name: BNRF1

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3221
Unit cell:
a: 161.216Å b: 161.216Å c: 117.772Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.237 0.234 0.28
Expression system: Escherichia coli BL21(DE3)