› 3ut9

X-ray diffraction
2.2Å resolution

Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)

Released:
DOI: 10.2210/pdb3ut9/pdb
PDB 3ut9 coloured by chain and viewed from the front.
PDB 3ut9 coloured by chain and viewed from the side.
PDB 3ut9 coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
The mechanics behind DNA sequence-dependent properties of the nucleosome.
Chua EY, Vasudevan D, Davey GE, Wu B, Davey CA
Nucleic Acids Res. (2012)
PMID: 22453276

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: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
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
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
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
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: 125 amino acids
Theoretical weight: 13.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
145-mer DNA Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.76 KDa
145-mer DNA Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.75 KDa

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand MN 29 x MN
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.494Å b: 109.533Å c: 174.822Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.257 0.256 0.289
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Biophysics of Chromatin Remodeling.
Nodelman et al. (2021)
9 more

14 mentions without citation

New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.
Zhou et al. (2015)
13 more