› 6c0w

Electron Microscopy
4Å resolution

Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A

Released:
DOI: 10.2210/pdb6c0w/pdb
PDB 6c0w coloured by chain and viewed from the front.
PDB 6c0w coloured by chain and viewed from the side.
PDB 6c0w coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Decoding the centromeric nucleosome through CENP-N.
Pentakota S, Zhou K, Smith C, Maffini S, Petrovic A, Morgan GP, Weir JR, Vetter IR, Musacchio A, Luger K
Elife 6 (2017)
PMID: 29280735
Related structures: EMD-7326

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P49450 (Residues: 1-140; Coverage: 100%)
Gene name: CENPA
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P62805 (Residues: 1-102; Coverage: 99%)
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, 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
Structure domains: Histone, subunit A
Histone H2A type 1-C Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93077 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC6, H2AFL, HIST1H2AC
Sequence domains:
Structure domains: Histone, subunit A
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
Structure domains: Histone, subunit A
Centromere protein N Chain: K
Molecule details ›
Chain: K
Length: 295 amino acids
Theoretical weight: 34.87 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: Q96H22 (Residues: 1-289; Coverage: 85%)
Gene names: BM-309, C16orf60, CENPN, ICEN32
147 mer DNA Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.15 KDa
147 mer DNA Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.59 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-7326
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Escherichia coli
  • Insect cell expression vector pTIE1

Quick links

Citations

5 review citations

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