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 8OW1 | pdb_00008ow1

Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere.

Dendooven, T., Zhang, Z., Yang, J., McLaughlin, S.H., Schwab, J., Scheres, S.H.W., Yatskevich, S., Barford, D.

(2023) Sci Adv 9: eadg7480-eadg7480

  • DOI: https://doi.org/10.1126/sciadv.adg7480
  • Primary Citation Related Structures: 
    8OVW, 8OVX, 8OW0, 8OW1

  • PubMed Abstract: 

    The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A Nuc ). This revealed a central CENP-A Nuc with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A Nuc can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle.


  • Organizational Affiliation: 
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 1,490.63 kDa 
  • Atom Count: 78,671 
  • Modeled Residue Count: 9,238 
  • Deposited Residue Count: 12,414 
  • Unique protein chains: 21
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere-binding protein 1
A, B
351Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CBF1, CEP1, CP1, CPF1, YJR060W, J1730
UniProt
Find proteins for P17106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF3AA [auth II],
C [auth I]
733Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF3, CHL3, YLR381W
UniProt
Find proteins for Q12748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM22BA [auth KK],
D [auth K]
239Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM22, YJR135C, J2122
UniProt
Find proteins for P47167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM16CA [auth HH],
E [auth H]
181Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM16, YPR046W
UniProt
Find proteins for Q12262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit IML3F [auth LL],
J [auth L]
245Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IML3, MCM19, YBR107C, YBR0836
UniProt
Find proteins for P38265 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CHL4G [auth NN],
P [auth N]
458Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CHL4, CTF17, MCM17, YDR254W, YD9320A.04
UniProt
Find proteins for P38907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit CH [auth CT]478Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF13, CBF3C, YMR094W, YM6543.01, YM9582.19
UniProt
Find proteins for P35203 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit BI [auth ce],
L [auth CE]
608Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C
UniProt
Find proteins for P40969 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1K [auth SK]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKP1, CBF3D, YDR328C, D9798.14
UniProt
Find proteins for P52286 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19M [auth P],
S [auth PP]
369Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF19, MCM18, YPL018W, LPB13W
UniProt
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1DA [auth QQ],
N [auth Q]
406Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OKP1, YGR179C
UniProt
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM21O [auth OO],
U [auth O]
368Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM21, CTF5, YDR318W
UniProt
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CNN1OA [auth TT],
Q [auth T]
361Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CNN1, YFR046C
UniProt
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1R [auth U],
X [auth UU]
324Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: AME1, ARP100, YBR211C, YBR1458
UniProt
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit WIP1PA [auth WW],
T [auth W]
89Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: WIP1, YDR374W-A
UniProt
Find proteins for Q2V2P8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP1V [auth Y],
Y [auth YY]
238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NKP1, YDR383C
UniProt
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP2W [auth Z],
Z [auth ZZ]
153Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NKP2, YLR315W
UniProt
Find proteins for Q06162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4GA [auth b],
JA [auth f]
103Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B.1HA [auth d],
LA [auth h]
131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTB1, H2B1, SPT12, YDR224C, YD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3-like centromeric protein CSE4IA [auth e],
NA [auth a]
229Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSE4, CSL2, YKL049C, YKL262
UniProt
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A.1KA [auth g],
MA [auth c]
132Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTA1, H2A1, SPT11, YDR225W, YD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 18
MoleculeChains LengthOrganismImage
C0N3EA [auth D]153Saccharomyces cerevisiae
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Entity ID: 19
MoleculeChains LengthOrganismImage
C0N3FA [auth E]153Saccharomyces cerevisiae
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMC_UP_1201/6
Cancer Research UKUnited KingdomC576/A14109
UK Research and Innovation (UKRI)United KingdomMC_UP_ A025_1013
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection