› 3lz1

X-ray diffraction
2.5Å resolution

Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2)

Released:
DOI: 10.2210/pdb3lz1/pdb
PDB 3lz1 coloured by chain and viewed from the front.
PDB 3lz1 coloured by chain and viewed from the side.
PDB 3lz1 coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Crystal structures of nucleosome core particles containing the '601' strong positioning sequence.
Vasudevan D, Chua EY, Davey CA
J. Mol. Biol. 403 1-10 (2010)
PMID: 20800598

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 Chains: C, G
Molecule details ›
Chains: C, G
Length: 119 amino acids
Theoretical weight: 12.94 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 2-120; Coverage: 92%)
Gene names: LOC494591, h2ac14, 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: 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
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.99 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.52 KDa

Ligands and Environments

2 bound ligands:
Ligand MN 6 x MN
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 107.37Å b: 109.66Å c: 175.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.27 0.269 0.319
Expression system: Escherichia coli

Quick links

Citations

14 review citations

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

18 mentions without citation

Nucleosome structural studies.
Tan et al. (2011)
17 more