8OVX | pdb_00008ovx

Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8OVX

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: 215.69 kDa 
  • Atom Count: 6,763 
  • Modeled Residue Count: 885 
  • Deposited Residue Count: 1,858 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM21A [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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19B [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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1C [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:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1D [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:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP1E [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:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP2F [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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.1: 2024-07-24
    Changes: Data collection
  • Version 1.2: 2025-07-09
    Changes: Data collection, Structure summary