› 5onw

X-ray diffraction
2.8Å resolution

X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C

Released:
DOI: 10.2210/pdb5onw/pdb
PDB 5onw coloured by chain and viewed from the front.
PDB 5onw coloured by chain and viewed from the side.
PDB 5onw coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.
Frouws TD, Barth PD, Richmond TJ
J. Mol. Biol. (2017)
PMID: 29113904

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.22 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
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: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
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: 13.97 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
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: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.43 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.42 KDa

Ligands and Environments

2 bound ligands:
Ligand MN 20 x MN
Ligand CL 4 x CL
1 modified residue:
Ligand G47 2 x G47

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 106.56Å b: 183.83Å c: 109.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 citation in other articles

Expressed Protein Ligation without Intein.
Qiao et al. (2020)
4 more

3 mentions without citation

Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.
Sanchez et al. (2021)
2 more