28OP | pdb_000028op

Structure of the human inner kinetochore CCAN and CENP-C bound to DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 28OP

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: 720.3 kDa 
  • Atom Count: 27,973 
  • Modeled Residue Count: 3,282 
  • Deposited Residue Count: 5,627 
  • Unique protein chains: 16
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein MA [auth M]180Homo sapiensMutation(s): 0 
Gene Names: CENPM
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Find proteins for Q9NSP4 (Homo sapiens)
Explore Q9NSP4 
Go to UniProtKB:  Q9NSP4
PHAROS:  Q9NSP4
GTEx:  ENSG00000100162 
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UniProt GroupQ9NSP4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein SB [auth S]138Homo sapiensMutation(s): 0 
Gene Names: CENPS
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Find proteins for Q8N2Z9 (Homo sapiens)
Explore Q8N2Z9 
Go to UniProtKB:  Q8N2Z9
PHAROS:  Q8N2Z9
GTEx:  ENSG00000175279 
Entity Groups
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UniProt GroupQ8N2Z9
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferase,Centromere protein TC [auth T]777Homo sapiensMutation(s): 0 
Gene Names: MGMTCENPTC16orf56ICEN22
EC: 2.1.1.63
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Find proteins for P16455 (Homo sapiens)
Explore P16455 
Go to UniProtKB:  P16455
PHAROS:  P16455
GTEx:  ENSG00000170430 
Find proteins for Q96BT3 (Homo sapiens)
Explore Q96BT3 
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PHAROS:  Q96BT3
GTEx:  ENSG00000102901 
Entity Groups
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UniProt GroupsP16455Q96BT3
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein UD [auth U]211Homo sapiensMutation(s): 0 
Gene Names: CENPUICEN24KLIP1MLF1IPPBIP1
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Find proteins for Q71F23 (Homo sapiens)
Explore Q71F23 
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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: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein WF [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: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein XG [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: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein HI [auth H]247Homo sapiensMutation(s): 0 
Gene Names: CENPH
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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: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein IJ [auth I]762Homo sapiensMutation(s): 0 
Gene Names: CENPIFSHPRH1ICEN19LRPR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92674 (Homo sapiens)
Explore Q92674 
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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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein K269Homo 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: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein L348Homo 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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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein NM [auth N]347Homo 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: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein ON [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: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein PO [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: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein QP [auth Q]215Trichoplusia niMutation(s): 0 
Gene Names: CENPQC6orf139
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2Z9 (Homo sapiens)
Explore Q7L2Z9 
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PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein RQ [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BP
UniProt & NIH Common Fund Data Resources
Find proteins for Q13352 (Homo sapiens)
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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: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein C,Methylated-DNA--protein-cysteine methyltransferaseR [auth C]775Homo sapiensMutation(s): 0 
Gene Names: CENPCMGMT
EC: 2.1.1.63
UniProt & NIH Common Fund Data Resources
Find proteins for Q03188 (Homo sapiens)
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PHAROS:  Q03188
GTEx:  ENSG00000145241 
Find proteins for P16455 (Homo sapiens)
Explore P16455 
Go to UniProtKB:  P16455
PHAROS:  P16455
GTEx:  ENSG00000170430 
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UniProt GroupsP16455Q03188
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (59-MER)E [auth V]212Homo sapiens
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Reference Sequence
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (61-MER)H [auth Y]212Homo sapiens
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.6

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