› 7ywx

Electron Microscopy
12Å resolution

Structure of the human CCAN CENP-A alpha-satellite complex

Released:
DOI: 10.2210/pdb7ywx/pdb
PDB entry 7ywx coloured by chain, front view.
PDB entry 7ywx coloured by chain, side view.
PDB entry 7ywx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D
Science 376 844-852 (2022)
PMID: 35420891
Related structures: EMD-14351

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-269923 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (22 distinct):
Centromere protein H Chain: H
Molecule details ›
Chain: H
Length: 247 amino acids
Theoretical weight: 28.52 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H3R5 (Residues: 1-247; Coverage: 100%)
Gene names: CENPH, ICEN35
Sequence domains: Centromere protein H (CENP-H)
Centromere protein I Chain: I
Molecule details ›
Chain: I
Length: 756 amino acids
Theoretical weight: 86.82 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92674 (Residues: 1-756; Coverage: 100%)
Gene names: CENPI, FSHPRH1, ICEN19, LRPR1
Sequence domains: Mis6
Centromere protein K Chain: K
Molecule details ›
Chain: K
Length: 269 amino acids
Theoretical weight: 31.7 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BS16 (Residues: 1-269; Coverage: 100%)
Gene names: CENPK, FKSG14, ICEN37
Sequence domains: Centromere-associated protein K
Centromere protein L Chain: L
Molecule details ›
Chain: L
Length: 344 amino acids
Theoretical weight: 39.04 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N0S6 (Residues: 1-344; Coverage: 100%)
Gene names: C1orf155, CENPL, ICEN33
Sequence domains: Kinetochore complex Sim4 subunit Fta1
Centromere protein M Chain: M
Molecule details ›
Chain: M
Length: 180 amino acids
Theoretical weight: 19.76 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NSP4 (Residues: 1-180; Coverage: 100%)
Gene names: C22orf18, CENPM, ICEN39, PANE1
Sequence domains: Centromere protein M (CENP-M)
Centromere protein N Chain: N
Molecule details ›
Chain: N
Length: 339 amino acids
Theoretical weight: 39.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96H22 (Residues: 1-339; Coverage: 100%)
Gene names: BM-309, C16orf60, CENPN, ICEN32
Sequence domains: Kinetochore protein CHL4 like
Centromere protein O Chain: O
Molecule details ›
Chain: O
Length: 300 amino acids
Theoretical weight: 33.83 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BU64 (Residues: 1-300; Coverage: 100%)
Gene names: CENPO, ICEN36, MCM21R
Sequence domains: Cenp-O kinetochore centromere component
Centromere protein Q Chain: Q
Molecule details ›
Chain: Q
Length: 268 amino acids
Theoretical weight: 30.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7L2Z9 (Residues: 1-268; Coverage: 100%)
Gene names: C6orf139, CENPQ
Sequence domains: CENP-Q, a CENPA-CAD centromere complex subunit
Centromere protein U Chain: U
Molecule details ›
Chain: U
Length: 418 amino acids
Theoretical weight: 47.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q71F23 (Residues: 1-418; Coverage: 100%)
Gene names: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1
Sequence domains: CENP-A nucleosome associated complex (NAC) subunit
Centromere protein P Chain: P
Molecule details ›
Chain: P
Length: 288 amino acids
Theoretical weight: 33.21 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6IPU0 (Residues: 1-288; Coverage: 100%)
Gene name: CENPP
Sequence domains: CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P
Centromere protein R Chain: R
Molecule details ›
Chain: R
Length: 177 amino acids
Theoretical weight: 20.23 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13352 (Residues: 1-177; Coverage: 100%)
Gene names: CENPR, ITGB3BP, NRIF3
Sequence domains: Kinetochore component, CENP-R
Centromere protein T Chain: T
Molecule details ›
Chain: T
Length: 561 amino acids
Theoretical weight: 60.5 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96BT3 (Residues: 1-561; Coverage: 100%)
Gene names: C16orf56, CENPT, ICEN22
Sequence domains:
Centromere protein W Chain: W
Molecule details ›
Chain: W
Length: 88 amino acids
Theoretical weight: 10.09 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q5EE01 (Residues: 1-88; Coverage: 100%)
Gene names: C6orf173, CENPW, CUG2
Sequence domains: CENP-W protein
Centromere protein S Chain: S
Molecule details ›
Chain: S
Length: 138 amino acids
Theoretical weight: 15.92 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N2Z9 (Residues: 1-138; Coverage: 100%)
Gene names: APITD1, CENPS, FAAP16, MHF1
Sequence domains: CENP-S protein
Centromere protein X Chain: X
Molecule details ›
Chain: X
Length: 81 amino acids
Theoretical weight: 8.97 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: A8MT69 (Residues: 1-81; Coverage: 100%)
Gene names: CENPX, FAAP10, MHF2, STRA13
Sequence domains: CENP-S associating Centromere protein X
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 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:
Histone H2B type 1-C/E/F/G/I Chains: D, V
Molecule details ›
Chains: D, V
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
Centromere protein C Chains: a, b
Molecule details ›
Chains: a, b
Length: 544 amino acids
Theoretical weight: 61.86 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03188 (Residues: 1-544; Coverage: 58%)
Gene names: CENPC, CENPC1, ICEN7
Sequence domains:
DNA (171-MER) Chain: i
Molecule details ›
Chain: i
Length: 171 nucleotides
Theoretical weight: 52.73 KDa
DNA (171-MER) Chain: J
Molecule details ›
Chain: J
Length: 171 nucleotides
Theoretical weight: 52.82 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 12Å
Relevant EMDB volumes: EMD-14351
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

6 review citations

The Four Causes: The Functional Architecture of Centromeres and Kinetochores.
McAinsh et al. (2022)
5 more

1 mention without citation

Centromeric chromatin clearings demarcate the site of kinetochore formation.
Kixmoeller et al. (2024)