› 5f99

X-ray diffraction
2.63Å resolution

X-ray Structure of the MMTV-A Nucleosome Core Particle

Released:
DOI: 10.2210/pdb5f99/pdb
PDB 5f99 coloured by chain and viewed from the front.
PDB 5f99 coloured by chain and viewed from the side.
PDB 5f99 coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
X-ray structure of the MMTV-A nucleosome core.
Frouws TD, Duda SC, Richmond TJ
Proc Natl Acad Sci U S A 113 1214-9 (2016)
PMID: 26787910

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: 15.27 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
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 BL21(DE3)
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 BL21(DE3)
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Structure domains: Histone, subunit A
DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 44.85 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.9 KDa

Ligands and Environments

2 bound ligands:
Ligand CL 4 x CL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 107.873Å b: 178.915Å c: 109.061Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.175 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

CENP-A nucleosome-a chromatin-embedded pedestal for the centromere: lessons learned from structural biology.
Ali-Ahmad et al. (2020)
4 more