› 6tem

Electron Microscopy
3.9Å resolution

CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM

Released:
DOI: 10.2210/pdb6tem/pdb
PDB entry 6tem coloured by chain, front view.
PDB entry 6tem coloured by chain, side view.
PDB entry 6tem coloured by chain, top view.
Source organisms:
Primary publication:
Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends.
Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S, Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C, Bednar J
Nucleic Acids Res 48 5735-5748 (2020)
PMID: 32313946
Related structures: EMD-10822

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-120648 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3-like centromeric protein A Chains: A, E
Molecule details ›
Chains: A, E
Length: 140 amino acids
Theoretical weight: 16.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49450 (Residues: 1-140; Coverage: 100%)
Gene name: CENPA
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
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: 125 amino acids
Theoretical weight: 13.83 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
Widom 601 DNA (145-MER, sense) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.55 KDa
Widom 601 DNA (145-MER, antisense) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.96 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-10822
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Unraveling linker histone interactions in nucleosomes.
Hao et al. (2021)
7 more

1 mention without citation

Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends.
Boopathi et al. (2020)