› 1zla

X-ray diffraction
2.9Å resolution

X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core

Released:
DOI: 10.2210/pdb1zla/pdb
PDB 1zla coloured by chain and viewed from the front.
PDB 1zla coloured by chain and viewed from the side.
PDB 1zla coloured by chain and viewed from the top.
Source organisms:
Primary publication:
The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA.
Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM
Science 311 856-61 (2006)
PMID: 16469929

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.34 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 14.18 KDa
Source organism: Expression vector pET3-H2A
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.79 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Latent nuclear antigen Chain: K
Molecule details ›
Chain: K
Length: 22 amino acids
Theoretical weight: 2.26 KDa
Source organism: Human gammaherpesvirus 8
Expression system: Not provided
UniProt:
  • Canonical: Q9DUM3 (Residues: 1-22; Coverage: 2%)
Palindromic 146bp Human alpha-Satellite DNA fragment 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: RIGAKU
Spacegroup: P212121
Unit cell:
a: 106.162Å b: 109.599Å c: 182.237Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.222 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

80 review citations

Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses.
Sato et al. (2022)
79 more

27 mentions without citation

Targeting the Nucleosome Acidic Patch by Viral Proteins: Two Birds with One Stone?
Lagadec et al. (2022)
26 more