› 3lja

X-ray diffraction
2.75Å resolution

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

Released:
DOI: 10.2210/pdb3lja/pdb
PDB 3lja coloured by chain and viewed from the front.
PDB 3lja coloured by chain and viewed from the side.
PDB 3lja coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome.
Wu B, Davey CA
J. Mol. Biol. 398 633-40 (2010)
PMID: 20350553

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: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
147mer DNA Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
147mer DNA Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.36 KDa

Ligands and Environments

2 bound ligands:
Ligand SO4 3 x SO4
Ligand MN 45 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.348Å b: 109.785Å c: 182.424Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.259
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence.
Vasudevan et al. (2010)
9 more

3 mentions without citation

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