› 3mgr

X-ray diffraction
2.3Å resolution

Binding of Rubidium ions to the Nucleosome Core Particle

Released:
DOI: 10.2210/pdb3mgr/pdb
PDB entry 3mgr coloured by chain, front view.
PDB entry 3mgr coloured by chain, side view.
PDB entry 3mgr coloured by chain, top view.
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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116567 (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.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

3 bound ligands:
Ligand CL 4 x CL
Ligand RB 5 x RB
Ligand MN 14 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 106.462Å b: 109.681Å c: 182.213Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.242 0.267
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Environmental epigenetics in metal exposure.
Martinez-Zamudio et al. (2011)
3 more

5 mentions without citation

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