› 3kwq

X-ray diffraction
3.5Å resolution

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays

Released:
DOI: 10.2210/pdb3kwq/pdb
PDB entry 3kwq coloured by chain, front view.
PDB entry 3kwq coloured by chain, side view.
PDB entry 3kwq coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.
Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K
Biochim Biophys Acta 1799 480-6
PMID: 20100606

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116508 (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: 98 amino acids
Theoretical weight: 11.5 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 39-136; Coverage: 72%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 83 amino acids
Theoretical weight: 9.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 21-103; Coverage: 81%)
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: 107 amino acids
Theoretical weight: 11.72 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 15-121; Coverage: 82%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 93 amino acids
Theoretical weight: 10.38 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 34-126; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
DNA (146-MER) 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: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 105.561Å b: 109.542Å c: 180.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.368 0.268 0.315
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Histone core modifications regulating nucleosome structure and dynamics.
Tessarz et al. (2014)
9 more

4 mentions without citation

Efficient and Innocuous Live-Cell Delivery: Making Membrane Barriers Disappear to Enable Cellular Biochemistry: How Better Cellular Delivery Tools Can Contribute to Precise and Quantitative Cell Biology Assays.
Pellois JP. (2019)
3 more