6YPC

Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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Literature

Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex.

Zhang, Z.Bellini, D.Barford, D.

(2020) Nucleic Acids Res 48: 11172-11184

  • DOI: 10.1093/nar/gkaa772
  • Primary Citation of Related Structures:  
    6YPC

  • PubMed Abstract: 
  • Kinetochores are large multi-subunit complexes that attach centromeric chromatin to microtubules of the mitotic spindle, enabling sister chromatid segregation in mitosis. The inner kinetochore constitutive centromere associated network (CCAN) complex assembles onto the centromere-specific Cenp-A nucleosome (Cenp-ANuc), thereby coupling the centromere to the microtubule-binding outer kinetochore ...

    Kinetochores are large multi-subunit complexes that attach centromeric chromatin to microtubules of the mitotic spindle, enabling sister chromatid segregation in mitosis. The inner kinetochore constitutive centromere associated network (CCAN) complex assembles onto the centromere-specific Cenp-A nucleosome (Cenp-ANuc), thereby coupling the centromere to the microtubule-binding outer kinetochore. CCAN is a conserved 14-16 subunit complex composed of discrete modules. Here, we determined the crystal structure of the Saccharomyces cerevisiae Cenp-HIKHead-TW sub-module, revealing how Cenp-HIK and Cenp-TW interact at the conserved Cenp-HIKHead-Cenp-TW interface. A major interface is formed by the C-terminal anti-parallel α-helices of the histone fold extension (HFE) of the Cenp-T histone fold domain (HFD) combining with α-helix H3 of Cenp-K to create a compact three α-helical bundle. We fitted the Cenp-HIKHead-TW sub-module to the previously determined cryo-EM map of the S. cerevisiae CCAN-Cenp-ANuc complex. This showed that the HEAT repeat domain of Cenp-IHead and C-terminal HFD of Cenp-T of the Cenp-HIKHead-TW sub-module interact with the nucleosome DNA gyre at a site close to the Cenp-ANuc dyad axis. Our structure provides a framework for understanding how Cenp-T links centromeric Cenp-ANuc to the outer kinetochore through its HFD and N-terminal Ndc80-binding motif, respectively.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM22A [auth K]110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM22YJR135CJ2122
UniProt
Find proteins for P47167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM16B [auth H]46Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM16YPR046W
UniProt
Find proteins for Q12262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit CNN1C [auth T]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CNN1YFR046C
UniProt
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit WIP1D [auth W]89Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: WIP1YDR374W-A
UniProt
Find proteins for Q2V2P8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF3E [auth I]251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF3CHL3YLR381W
UniProt
Find proteins for Q12748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.577α = 90
b = 132.577β = 90
c = 241.676γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6
Cancer Research UKC576/A14109

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references