› 6se0

Electron Microscopy
3.8Å resolution

Class 1 : CENP-A nucleosome

Released:
DOI: 10.2210/pdb6se0/pdb
PDB entry 6se0 coloured by chain, front view.
PDB entry 6se0 coloured by chain, side view.
PDB entry 6se0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Ali-Ahmad A, Bilokapić S, Schäfer IB, Halić M, Sekulić N
EMBO Rep 20 e48913 (2019)
PMID: 31475439
Related structures: EMD-10151

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-120605 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 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: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 2-A Chain: C
Molecule details ›
Chain: C
Length: 129 amino acids
Theoretical weight: 13.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6FI13 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC18, H2AC19, H2AFO, HIST2H2AA, HIST2H2AA3, HIST2H2AA4
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62807 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2A type 2-A Chain: G
Molecule details ›
Chain: G
Length: 130 amino acids
Theoretical weight: 14.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6FI13 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC18, H2AC19, H2AFO, HIST2H2AA, HIST2H2AA3, HIST2H2AA4
Sequence domains:
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: 3.8Å
Relevant EMDB volumes: EMD-10151
Expression system: Escherichia coli

Quick links

Citations

3 review citations

CENP-A Regulation and Cancer.
Renaud-Pageot et al. (2022)
2 more

3 mentions without citation

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