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 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

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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: 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: MCM21, CTF5, YDR318W
UniProt
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06675 
Go to UniProtKB:  Q06675
Entity Groups
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UniProt GroupQ06675
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19B [auth P]369Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF19, MCM18, YPL018W, LPB13W
UniProt
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02732 
Go to UniProtKB:  Q02732
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UniProt GroupQ02732
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1C [auth Q]406Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OKP1, YGR179C
UniProt
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53298 
Go to UniProtKB:  P53298
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UniProt GroupP53298
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1D [auth U]324Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: AME1, ARP100, YBR211C, YBR1458
UniProt
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38313 
Go to UniProtKB:  P38313
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UniProt GroupP38313
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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: NKP1, YDR383C
UniProt
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12493 
Go to UniProtKB:  Q12493
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UniProt GroupQ12493
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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: NKP2, YLR315W
UniProt
Find proteins for Q06162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06162 
Go to UniProtKB:  Q06162
Entity Groups
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UniProt GroupQ06162
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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

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