› 4ys3

X-ray diffraction
3Å resolution

Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis

Released:
DOI: 10.2210/pdb4ys3/pdb
PDB entry 4ys3 coloured by chain, front view.
PDB entry 4ys3 coloured by chain, side view.
PDB entry 4ys3 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF.
Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew B
Mol Cell Biol 35 4083-92 (2015)
PMID: 26416878

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-118342 (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: 98 amino acids
Theoretical weight: 11.58 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: 79 amino acids
Theoretical weight: 8.91 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 25-103; Coverage: 77%)
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 (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.36 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand ALY 4 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 105.51Å b: 109.62Å c: 181.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.279
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Biophysics of Chromatin Dynamics.
Fierz et al. (2019)
4 more

1 mention without citation

Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies.
Musselman et al. (2019)