8OVW

Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centromere-binding protein 1
A, B
351Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CBF1CEP1CP1CPF1YJR060WJ1730
UniProt
Find proteins for P17106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17106 
Go to UniProtKB:  P17106
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17106
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM16D [auth H]181Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM16YPR046W
UniProt
Find proteins for Q12262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12262 
Go to UniProtKB:  Q12262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12262
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF3E [auth I]733Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF3CHL3YLR381W
UniProt
Find proteins for Q12748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12748 
Go to UniProtKB:  Q12748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12748
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM22F [auth K]239Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM22YJR135CJ2122
UniProt
Find proteins for P47167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47167 
Go to UniProtKB:  P47167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47167
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit IML3G [auth L]245Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IML3MCM19YBR107CYBR0836
UniProt
Find proteins for P38265 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38265 
Go to UniProtKB:  P38265
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38265
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CHL4H [auth N]458Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CHL4CTF17MCM17YDR254WYD9320A.04
UniProt
Find proteins for P38907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38907 
Go to UniProtKB:  P38907
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38907
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM21I [auth O]368Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM21CTF5YDR318W
UniProt
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06675 
Go to UniProtKB:  Q06675
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06675
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19J [auth P]369Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF19MCM18YPL018WLPB13W
UniProt
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02732 
Go to UniProtKB:  Q02732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02732
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1K [auth Q]406Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OKP1YGR179C
UniProt
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53298 
Go to UniProtKB:  P53298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53298
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CNN1L [auth T]361Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CNN1YFR046C
UniProt
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43618 
Go to UniProtKB:  P43618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43618
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1M [auth U]324Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: AME1ARP100YBR211CYBR1458
UniProt
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38313 
Go to UniProtKB:  P38313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit WIP1N [auth W]89Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: WIP1YDR374W-A
UniProt
Find proteins for Q2V2P8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q2V2P8 
Go to UniProtKB:  Q2V2P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2V2P8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP1O [auth Y]238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NKP1YDR383C
UniProt
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12493 
Go to UniProtKB:  Q12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12493
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP2P [auth Z]153Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NKP2YLR315W
UniProt
Find proteins for Q06162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06162 
Go to UniProtKB:  Q06162
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06162
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
C0N3 DNAC [auth D]153Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
C0N3 DNAQ [auth E]153Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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