› 7wlr

Electron Microscopy
3.54Å resolution

Cryo-EM structure of the nucleosome containing Komagataella pastoris histones

Released:
DOI: 10.2210/pdb7wlr/pdb
PDB entry 7wlr coloured by chain, front view.
PDB entry 7wlr coloured by chain, side view.
PDB entry 7wlr coloured by chain, top view.
Source organism: Komagataella pastoris
Primary publication:
Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones.
Fukushima Y, Hatazawa S, Hirai S, Kujirai T, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H
J Biochem (2022)
PMID: 35485963
Related structures: EMD-32591

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-103261 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 99 amino acids
Theoretical weight: 11.6 KDa
Source organism: Komagataella pastoris
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1B2JB78 (Residues: 39-137; Coverage: 72%)
Gene names: ATY40_BA7502079, ATY40_BA7504318
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 87 amino acids
Theoretical weight: 10.03 KDa
Source organism: Komagataella pastoris
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1B2JA70 (Residues: 17-103; Coverage: 85%)
Gene names: ATY40_BA7502080, ATY40_BA7504319
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 108 amino acids
Theoretical weight: 11.81 KDa
Source organism: Komagataella pastoris
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1B2JD99 (Residues: 13-120; Coverage: 83%)
Gene names: ATY40_BA7502752, HTA1
Sequence domains:
Histone H2B Chains: D, H
Molecule details ›
Chains: D, H
Length: 99 amino acids
Theoretical weight: 11.02 KDa
Source organism: Komagataella pastoris
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1B2JBS1 (Residues: 34-132; Coverage: 75%)
Gene name: ATY40_BA7502753
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.54Å
Relevant EMDB volumes: EMD-32591
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses.
Sato et al. (2022)
1 more

3 mentions without citation

Nucleosomes at the Dawn of Eukaryotes.
Hocher et al. (2024)
2 more