› 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 entry 1zla coloured by chain, front view.
PDB entry 1zla coloured by chain, side view.
PDB entry 1zla coloured by chain, top view.
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:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-114923 (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
Protein LANA1-like DNA-binding domain-containing protein 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

84 review citations

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?
Luger et al. (2012)
83 more

28 mentions without citation

Nucleosome structure and function.
McGinty et al. (2015)
27 more