› 7swy

Electron Microscopy
2.6Å resolution

2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome

Released:
DOI: 10.2210/pdb7swy/pdb
PDB entry 7swy coloured by chain, front view.
PDB entry 7swy coloured by chain, side view.
PDB entry 7swy coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state.
Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP
Nat Struct Mol Biol 29 121-129 (2022)
PMID: 35173352
Related structures: EMD-25479

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-122045 (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
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
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
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:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.54 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
DNA Tracking Strand Chain: I
Molecule details ›
Chain: I
Length: 226 nucleotides
Theoretical weight: 69.5 KDa
DNA Guide Strand Chain: J
Molecule details ›
Chain: J
Length: 226 nucleotides
Theoretical weight: 70.07 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.6Å
Relevant EMDB volumes: EMD-25479
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Chicken Erythrocyte: Epigenomic Regulation of Gene Activity.
Beacon et al. (2023)
2 more

1 mention without citation

Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state.
Nodelman et al. (2022)