› 5ong

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

Released:
DOI: 10.2210/pdb5ong/pdb
PDB entry 5ong coloured by chain, front view.
PDB entry 5ong coloured by chain, side view.
PDB entry 5ong coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.
Frouws TD, Barth PD, Richmond TJ
J Mol Biol 430 45-57 (2018)
PMID: 29113904

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-119106 (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: 13.98 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 X06SA
Spacegroup: P212121
Unit cell:
a: 106.24Å b: 183.13Å c: 109.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.206 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

Automated cryo-EM structure refinement using correlation-driven molecular dynamics.
Igaev et al. (2019)
6 more

1 mention without citation

Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.
Frouws et al. (2018)