6GYS

Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history. 


Literature

Architecture of the CBF3-centromere complex of the budding yeast kinetochore.

Yan, K., Zhang, Z., Yang, J., McLaughlin, S.H., Barford, D.

(2018) Nat Struct Mol Biol 25: 1103-1110

  • DOI: 10.1038/s41594-018-0154-1
  • Primary Citation of Related Structures:  
    6GYP, 6GYS, 6GYU

  • PubMed Abstract: 

    • Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4 ...

    Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge, UK. dbarford@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit CA, H478Saccharomyces 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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UniProt GroupP35203
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit BB, C, I, J608Saccharomyces 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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UniProt GroupP40969
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1D, K194Saccharomyces 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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UniProt GroupP52286
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Centromere DNA-binding protein complex CBF3 subunit AE, L956Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CBF2, CBF3A, CEP2, CTF14, NDC10, YGR140W
UniProt
Find proteins for P32504 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (52-MER)F52Saccharomyces cerevisiae
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (52-MER)G52Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMRC_UP_1201/6
Cancer Research UKUnited KingdomC576/A14109

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations, Experimental preparation
  • Version 1.3: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other