7YWX | pdb_00007ywx

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7YWX

This is version 1.2 of the entry. See complete history

Literature

Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.

Yatskevich, S.Muir, K.W.Bellini, D.Zhang, Z.Yang, J.Tischer, T.Predin, M.Dendooven, T.McLaughlin, S.H.Barford, D.

(2022) Science 376: 844-852

  • DOI: https://doi.org/10.1126/science.abn3810
  • Primary Citation Related Structures: 
    7PB4, 7PB8, 7PII, 7PKN, 7R5R, 7R5S, 7R5V, 7YWX, 7YYH

  • PubMed Abstract: 

    Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A Nuc ) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A Nuc reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A Nuc , and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 846.7 kDa 
  • Atom Count: 38,294 
  • Modeled Residue Count: 4,264 
  • Deposited Residue Count: 6,882 
  • Unique protein chains: 20
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein HA [auth H]247Homo sapiensMutation(s): 0 
Gene Names: CENPHICEN35
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Find proteins for Q9H3R5 (Homo sapiens)
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PHAROS:  Q9H3R5
GTEx:  ENSG00000153044 
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UniProt GroupQ9H3R5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein IB [auth I]756Homo sapiensMutation(s): 0 
Gene Names: CENPIFSHPRH1ICEN19LRPR1
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Find proteins for Q92674 (Homo sapiens)
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PHAROS:  Q92674
GTEx:  ENSG00000102384 
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UniProt GroupQ92674
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein KC [auth K]269Homo sapiensMutation(s): 0 
Gene Names: CENPKICEN37FKSG14
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Find proteins for Q9BS16 (Homo sapiens)
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PHAROS:  Q9BS16
GTEx:  ENSG00000123219 
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UniProt GroupQ9BS16
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein LD [auth L]344Homo sapiensMutation(s): 0 
Gene Names: CENPLC1orf155ICEN33
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Find proteins for Q8N0S6 (Homo sapiens)
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PHAROS:  Q8N0S6
GTEx:  ENSG00000120334 
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UniProt GroupQ8N0S6
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein ME [auth M]180Homo sapiensMutation(s): 0 
Gene Names: CENPMC22orf18ICEN39PANE1
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Find proteins for Q9NSP4 (Homo sapiens)
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PHAROS:  Q9NSP4
GTEx:  ENSG00000100162 
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UniProt GroupQ9NSP4
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein NF [auth N]339Homo sapiensMutation(s): 0 
Gene Names: CENPNC16orf60ICEN32BM-309
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Find proteins for Q96H22 (Homo sapiens)
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PHAROS:  Q96H22
GTEx:  ENSG00000166451 
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UniProt GroupQ96H22
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein OG [auth O]300Homo sapiensMutation(s): 0 
Gene Names: CENPOICEN36MCM21R
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Find proteins for Q9BU64 (Homo sapiens)
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PHAROS:  Q9BU64
GTEx:  ENSG00000138092 
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UniProt GroupQ9BU64
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein QH [auth Q]268Homo sapiensMutation(s): 0 
Gene Names: CENPQC6orf139
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Find proteins for Q7L2Z9 (Homo sapiens)
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PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
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UniProt GroupQ7L2Z9
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein UI [auth U]418Homo sapiensMutation(s): 0 
Gene Names: CENPUICEN24KLIP1MLF1IPPBIP1
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Find proteins for Q71F23 (Homo sapiens)
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PHAROS:  Q71F23
GTEx:  ENSG00000151725 
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UniProt GroupQ71F23
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein PJ [auth P]288Homo sapiensMutation(s): 0 
Gene Names: CENPP
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Find proteins for Q6IPU0 (Homo sapiens)
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PHAROS:  Q6IPU0
GTEx:  ENSG00000188312 
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UniProt GroupQ6IPU0
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein RK [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BPCENPRNRIF3
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Find proteins for Q13352 (Homo sapiens)
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PHAROS:  Q13352
GTEx:  ENSG00000142856 
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UniProt GroupQ13352
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein TL [auth T]561Homo sapiensMutation(s): 0 
Gene Names: CENPTC16orf56ICEN22
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Find proteins for Q96BT3 (Homo sapiens)
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PHAROS:  Q96BT3
GTEx:  ENSG00000102901 
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UniProt GroupQ96BT3
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein WM [auth W]88Homo sapiensMutation(s): 0 
Gene Names: CENPWC6orf173CUG2
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Find proteins for Q5EE01 (Homo sapiens)
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PHAROS:  Q5EE01
GTEx:  ENSG00000203760 
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UniProt GroupQ5EE01
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein SN [auth S]138Homo sapiensMutation(s): 0 
Gene Names: CENPSAPITD1FAAP16MHF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N2Z9 (Homo sapiens)
Explore Q8N2Z9 
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PHAROS:  Q8N2Z9
GTEx:  ENSG00000175279 
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UniProt GroupQ8N2Z9
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein XO [auth X]81Homo sapiensMutation(s): 0 
Gene Names: CENPXFAAP10MHF2STRA13
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Find proteins for A8MT69 (Homo sapiens)
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PHAROS:  A8MT69
GTEx:  ENSG00000169689 
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UniProt GroupA8MT69
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AR [auth A],
V [auth E]
140Homo sapiensMutation(s): 0 
Gene Names: CENPA
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Find proteins for P49450 (Homo sapiens)
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PHAROS:  P49450
GTEx:  ENSG00000115163 
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UniProt GroupP49450
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4S [auth B],
W [auth F]
103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-CT [auth C],
X [auth G]
130Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
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Find proteins for Q93077 (Homo sapiens)
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PHAROS:  Q93077
GTEx:  ENSG00000180573 
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UniProt GroupQ93077
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IU [auth D],
Y [auth V]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
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Find proteins for P62807 (Homo sapiens)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein CAA [auth b],
Z [auth a]
544Homo sapiensMutation(s): 0 
Gene Names: CENPCCENPC1ICEN7
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Find proteins for Q03188 (Homo sapiens)
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PHAROS:  Q03188
GTEx:  ENSG00000145241 
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UniProt GroupQ03188
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Reference Sequence
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (171-MER)P [auth i]171Homo sapiens
Sequence Annotations
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Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (171-MER)Q [auth J]171Homo sapiens
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--
Boehringer Ingelheim Fonds (BIF)Germany--
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection