6QLF | pdb_00006qlf

Structure of inner kinetochore CCAN complex with mask1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history

Literature

Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome.

Yan, K.Yang, J.Zhang, Z.McLaughlin, S.H.Chang, L.Fasci, D.Ehrenhofer-Murray, A.E.Heck, A.J.R.Barford, D.

(2019) Nature 574: 278-282

  • DOI: https://doi.org/10.1038/s41586-019-1609-1
  • Primary Citation Related Structures: 
    6QLD, 6QLE, 6QLF

  • PubMed Abstract: 

    In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes 1,2 , function to connect centromeric chromatin to microtubules of the mitotic spindle 3,4 . Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules 5,6 . All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A Nuc ), each of which is perfectly centred on its cognate centromere 7-9 . The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A Nuc ). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A Nuc to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A Nuc are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A Nuc . Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 296.89 kDa 
  • Atom Count: 13,501 
  • Modeled Residue Count: 1,783 
  • Deposited Residue Count: 2,563 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit IML3A [auth L]245Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: IML3MCM19YBR107CYBR0836
UniProt
Find proteins for P38265 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38265
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UniProt GroupP38265
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CHL4B [auth N]464Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CHL4CTF17MCM17YDR254WYD9320A.04
UniProt
Find proteins for P38907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38907 
Go to UniProtKB:  P38907
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UniProt GroupP38907
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM21C [auth O]368Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM21CTF5YDR318W
UniProt
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06675 
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UniProt GroupQ06675
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19D [auth P]369Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF19MCM18YPL018WLPB13W
UniProt
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02732
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UniProt GroupQ02732
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1E [auth Q]406Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OKP1YGR179C
UniProt
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53298
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1F [auth U]320Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: AME1ARP100YBR211CYBR1458
UniProt
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP1G [auth Y]238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NKP1YDR383C
UniProt
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ12493
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP2H [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
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UniProt GroupQ06162
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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
Medical Research Council (United Kingdom)United KingdomMC_UP_1201/6
Cancer Research UKUnited KingdomC576/A14109
European CommissionINFRAIA project Epic-XS (Project 823839)

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references
  • Version 1.4: 2025-07-09
    Changes: Data collection, Structure summary