8OW1

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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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 of 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere-binding protein 1
A, B
351Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CBF1CEP1CP1CPF1YJR060WJ1730
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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: CTF3CHL3YLR381W
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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: MCM22YJR135CJ2122
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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: MCM16YPR046W
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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: IML3MCM19YBR107CYBR0836
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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: CHL4CTF17MCM17YDR254WYD9320A.04
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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: CTF13CBF3CYMR094WYM6543.01YM9582.19
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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: CEP3CBF3CBF3BCSL1YMR168CYM8520.17C
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1K [auth SK]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKP1CBF3DYDR328CD9798.14
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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: CTF19MCM18YPL018WLPB13W
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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: OKP1YGR179C
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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: MCM21CTF5YDR318W
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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: CNN1YFR046C
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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: AME1ARP100YBR211CYBR1458
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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: WIP1YDR374W-A
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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: NKP1YDR383C
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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: NKP2YLR315W
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4GA [auth b],
JA [auth f]
103Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.1HA [auth d],
LA [auth h]
131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09C
UniProt
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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: CSE4CSL2YKL049CYKL262
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.1KA [auth g],
MA [auth c]
132Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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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Experimental Data & Validation

Experimental Data

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

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