› 3mgq

X-ray diffraction
2.65Å resolution

Binding of Nickel ions to the Nucleosome Core Particle

Released:
DOI: 10.2210/pdb3mgq/pdb
PDB 3mgq coloured by chain and viewed from the front.
PDB 3mgq coloured by chain and viewed from the side.
PDB 3mgq coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Perturbations in nucleosome structure from heavy metal association.
Mohideen K, Muhammad R, Davey CA
Nucleic Acids Res. 38 6301-11 (2010)
PMID: 20494975

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 (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

2 bound ligands:
Ligand NI 47 x NI
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.129Å b: 109.643Å c: 183.109Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.232 0.276
Expression system: Escherichia coli

Quick links

Citations

4 review citations

DNA methylation changes induced by prenatal toxic metal exposure: An overview of epidemiological evidence.
Vaiserman et al. (2021)
3 more

2 mentions without citation

Perturbations in nucleosome structure from heavy metal association.
Mohideen et al. (2010)
1 more