› 6fq5

Electron Microscopy
3.8Å resolution

Class 1 : canonical nucleosome

Released:
DOI: 10.2210/pdb6fq5/pdb
PDB entry 6fq5 coloured by chain, front view.
PDB entry 6fq5 coloured by chain, side view.
PDB entry 6fq5 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structural rearrangements of the histone octamer translocate DNA.
Bilokapic S, Strauss M, Halic M
Nat Commun 9 1330 (2018)
PMID: 29626188
Related structures: EMD-4297

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119914 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 98 amino acids
Theoretical weight: 11.56 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 38-135; Coverage: 72%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 84 amino acids
Theoretical weight: 9.65 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 19-102; Coverage: 82%)
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: 110 amino acids
Theoretical weight: 12.08 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 10-119; Coverage: 85%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 95 amino acids
Theoretical weight: 10.64 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 31-125; Coverage: 75%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chain: F
Molecule details ›
Chain: F
Length: 85 amino acids
Theoretical weight: 9.7 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 19-103; Coverage: 83%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.6 KDa
DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.15 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-4297
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Biophysics of Chromatin Remodeling.
Nodelman et al. (2021)
7 more

7 mentions without citation

Histone variants and chromatin structure, update of advances.
Sokolova et al. (2023)
6 more