9TAX | pdb_00009tax

Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Models for the architecture of the human inner kinetochore on centromeric alpha-satellite CENP-A nucleosome arrays.

Yu, C.Muir, K.W.Yang, J.Zhang, Z.McLaughlin, S.H.Barford, D.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-72856-0
  • Primary Citation Related Structures: 
    28OP, 9TAW, 9TAX, 9TAY

  • PubMed Abstract: 

    Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled onto α-satellite arrays, we show cryo-EM structures of CCAN with free DNA, and α-satellite repeat monomers and dimers with CENP-A nucleosomes. CCAN bound to free DNA and a monomeric CENP-A nucleosome engages 70 bp of DNA comprising 30 bp of an upstream α-satellite repeat. This upstream DNA interacts with the histone-fold domain subunits of the CENP-TWSX module in a manner resembling how nucleosomes wrap DNA gyres. A complex of CCAN assembled onto a dimeric α-satellite repeat with two CENP-A nucleosomes shows that CCAN can only be accommodated on the linker DNA by unwrapping DNA from both the CENP-TWSX module and the upstream nucleosome. We discuss the implications of these results for models of CCAN assembly on arrays of α-satellite chromatin containing CENP-A nucleosomes.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 922.82 kDa 
  • Atom Count: 40,202 
  • Modeled Residue Count: 4,360 
  • Deposited Residue Count: 7,446 
  • 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: CENPH
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R5 (Homo sapiens)
Explore Q9H3R5 
Go to UniProtKB:  Q9H3R5
PHAROS:  Q9H3R5
GTEx:  ENSG00000153044 
Entity Groups
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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]762Homo sapiensMutation(s): 0 
Gene Names: CENPI
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Find proteins for A0A8C8KX99 (Homo sapiens)
Explore A0A8C8KX99 
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GTEx:  ENSG00000102384 
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UniProt GroupA0A8C8KX99
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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: CENPK
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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 MD [auth M]180Homo sapiensMutation(s): 0 
Gene Names: CENPM
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Find proteins for Q9NSP4 (Homo sapiens)
Explore Q9NSP4 
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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: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein LE [auth L]348Homo sapiensMutation(s): 0 
Gene Names: CENPLC1orf155ICEN33
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Find proteins for Q8N0S6 (Homo sapiens)
Explore Q8N0S6 
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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: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 3 of Centromere protein NF [auth N]347Homo sapiensMutation(s): 0 
Gene Names: CENPNC16orf60ICEN32BM-309
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H22 (Homo sapiens)
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451 
Entity Groups
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UniProt GroupQ96H22-3
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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: CENPO
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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 PH [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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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein QI [auth Q]215Homo sapiensMutation(s): 0 
Gene Names: CENPQC6orf139
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Find proteins for Q7L2Z9 (Homo sapiens)
Explore Q7L2Z9 
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PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
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UniProt GroupQ7L2Z9
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein UJ [auth U]211Homo 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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein RK [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BP
UniProt & NIH Common Fund Data Resources
Find proteins for Q13352 (Homo sapiens)
Explore Q13352 
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PHAROS:  Q13352
GTEx:  ENSG00000142856 
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UniProt GroupQ13352
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein TL [auth T]777Homo 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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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein WM [auth W]88Homo sapiensMutation(s): 0 
Gene Names: CENPW
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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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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein SN [auth S]138Homo sapiensMutation(s): 0 
Gene Names: CENPS
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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: CENPX
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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
Centromere protein CR [auth a],
S [auth b]
775Homo sapiensMutation(s): 0 
Gene Names: CENPC
UniProt & NIH Common Fund Data Resources
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: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein AT [auth c],
X [auth g]
140Homo sapiensMutation(s): 0 
Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
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: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4U [auth d],
Y [auth h]
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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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-CV [auth e],
Z [auth i]
153Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
Explore Q93077 
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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: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IAA [auth j],
W [auth f]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
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UniProt GroupP62807
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Reference Sequence
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (199-MER)P [auth V]212Homo sapiens
Sequence Annotations
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Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (199-MER)Q [auth Y]212Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_120
Cancer Research UKUnited KingdomC576/A25675

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release