9TAY | pdb_00009tay

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9TAY

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: 1,051.77 kDa 
  • Atom Count: 57,462 
  • Modeled Residue Count: 6,201 
  • Deposited Residue Count: 8,228 
  • Unique protein chains: 20
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein HA [auth H]247Homo sapiensMutation(s): 0 
Gene Names: CENPHICEN35
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R5 (Homo sapiens)
Explore Q9H3R5 
Go to UniProtKB:  Q9H3R5
PHAROS:  Q9H3R5
GTEx:  ENSG00000153044 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3R5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein IB [auth I]762Homo sapiensMutation(s): 0 
Gene Names: CENPIFSHPRH1ICEN19LRPR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92674 (Homo sapiens)
Explore Q92674 
Go to UniProtKB:  Q92674
PHAROS:  Q92674
GTEx:  ENSG00000102384 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92674
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein KC [auth K]269Homo sapiensMutation(s): 0 
Gene Names: CENPKICEN37FKSG14
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BS16 (Homo sapiens)
Explore Q9BS16 
Go to UniProtKB:  Q9BS16
PHAROS:  Q9BS16
GTEx:  ENSG00000123219 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BS16
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein LD [auth L]348Homo sapiensMutation(s): 0 
Gene Names: CENPLC1orf155ICEN33
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N0S6 (Homo sapiens)
Explore Q8N0S6 
Go to UniProtKB:  Q8N0S6
PHAROS:  Q8N0S6
GTEx:  ENSG00000120334 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N0S6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein ME [auth M]180Homo sapiensMutation(s): 0 
Gene Names: CENPMC22orf18ICEN39PANE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NSP4 (Homo sapiens)
Explore Q9NSP4 
Go to UniProtKB:  Q9NSP4
PHAROS:  Q9NSP4
GTEx:  ENSG00000100162 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NSP4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
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)
Explore Q96H22 
Go to UniProtKB:  Q96H22
PHAROS:  Q96H22
GTEx:  ENSG00000166451 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96H22
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein OG [auth O]300Homo sapiensMutation(s): 0 
Gene Names: CENPOICEN36MCM21R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BU64 (Homo sapiens)
Explore Q9BU64 
Go to UniProtKB:  Q9BU64
PHAROS:  Q9BU64
GTEx:  ENSG00000138092 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BU64
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein QH [auth Q]215Homo sapiensMutation(s): 0 
Gene Names: CENPQC6orf139
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2Z9 (Homo sapiens)
Explore Q7L2Z9 
Go to UniProtKB:  Q7L2Z9
PHAROS:  Q7L2Z9
GTEx:  ENSG00000031691 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L2Z9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein UI [auth U]211Homo sapiensMutation(s): 0 
Gene Names: CENPUICEN24KLIP1MLF1IPPBIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q71F23 (Homo sapiens)
Explore Q71F23 
Go to UniProtKB:  Q71F23
PHAROS:  Q71F23
GTEx:  ENSG00000151725 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71F23
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein PJ [auth P]288Homo sapiensMutation(s): 0 
Gene Names: CENPP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IPU0 (Homo sapiens)
Explore Q6IPU0 
Go to UniProtKB:  Q6IPU0
PHAROS:  Q6IPU0
GTEx:  ENSG00000188312 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IPU0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein RK [auth R]177Homo sapiensMutation(s): 0 
Gene Names: ITGB3BPCENPRNRIF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13352 (Homo sapiens)
Explore Q13352 
Go to UniProtKB:  Q13352
PHAROS:  Q13352
GTEx:  ENSG00000142856 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13352
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferase,Centromere protein TL [auth T]777Homo sapiensMutation(s): 0 
Gene Names: MGMTCENPTC16orf56ICEN22
EC: 2.1.1.63
UniProt & NIH Common Fund Data Resources
Find proteins for P16455 (Homo sapiens)
Explore P16455 
Go to UniProtKB:  P16455
PHAROS:  P16455
GTEx:  ENSG00000170430 
Find proteins for Q96BT3 (Homo sapiens)
Explore Q96BT3 
Go to UniProtKB:  Q96BT3
PHAROS:  Q96BT3
GTEx:  ENSG00000102901 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP16455Q96BT3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein WM [auth W]88Homo sapiensMutation(s): 0 
Gene Names: CENPWC6orf173CUG2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5EE01 (Homo sapiens)
Explore Q5EE01 
Go to UniProtKB:  Q5EE01
PHAROS:  Q5EE01
GTEx:  ENSG00000203760 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EE01
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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 
Go to UniProtKB:  Q8N2Z9
PHAROS:  Q8N2Z9
GTEx:  ENSG00000175279 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N2Z9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere protein XO [auth X]81Homo sapiensMutation(s): 0 
Gene Names: CENPXFAAP10MHF2STRA13
UniProt & NIH Common Fund Data Resources
Find proteins for A8MT69 (Homo sapiens)
Explore A8MT69 
Go to UniProtKB:  A8MT69
PHAROS:  A8MT69
GTEx:  ENSG00000169689 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8MT69
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein ABA [auth c],
FA [auth g],
P [auth A],
T [auth E]
140Homo sapiensMutation(s): 0 
Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens)
Explore P49450 
Go to UniProtKB:  P49450
PHAROS:  P49450
GTEx:  ENSG00000115163 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49450
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4CA [auth d],
GA [auth h],
Q [auth B],
U [auth F]
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-CDA [auth e],
HA [auth i],
R [auth C],
V [auth G]
153Homo sapiensMutation(s): 0 
Gene Names: H2AC6H2AFLHIST1H2AC
UniProt & NIH Common Fund Data Resources
Find proteins for Q93077 (Homo sapiens)
Explore Q93077 
Go to UniProtKB:  Q93077
PHAROS:  Q93077
GTEx:  ENSG00000180573 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93077
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IEA [auth f],
IA [auth j],
S [auth D],
W [auth J]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62807
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
scFvAA [auth a],
JA [auth m],
KA [auth n],
Z
266Mus musculusMutation(s): 0 
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 20
MoleculeChains LengthOrganismImage
DNA (318-MER)X [auth V]324Homo sapiens
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 21
MoleculeChains LengthOrganismImage
DNA (318-MER)324Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



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