› 3kxb

X-ray diffraction
3.2Å resolution

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays

Released:
DOI: 10.2210/pdb3kxb/pdb
PDB entry 3kxb coloured by chain, front view.
PDB entry 3kxb coloured by chain, side view.
PDB entry 3kxb 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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116509 (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: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
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 BL21
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6AZJ8 (Residues: 2-130; Coverage: 99%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE 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: RIGAKU RUH3R
Spacegroup: P212121
Unit cell:
a: 109.517Å b: 105.67Å c: 181.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.378 0.284 0.292
Expression system: Escherichia coli BL21

Quick links

Citations

10 review citations

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

2 mentions without citation

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.
Watanabe et al. (2010)
1 more