6QLD

Structure of inner kinetochore CCAN-Cenp-A complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1038/s41586-019-1609-1
  • Primary Citation of 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 ...

    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. dbarford@mrc-lmb.cam.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MIF2A [auth C]22Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MIF2YKL089W
UniProt
Find proteins for P35201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35201 
Go to UniProtKB:  P35201
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM16C [auth H]133Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM16YPR046W
UniProt
Find proteins for Q12262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12262 
Go to UniProtKB:  Q12262
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF3D [auth I]408Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF3CHL3YLR381W
UniProt
Find proteins for Q12748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12748 
Go to UniProtKB:  Q12748
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM22F [auth K]122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM22YJR135CJ2122
UniProt
Find proteins for P47167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47167 
Go to UniProtKB:  P47167
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit IML3G [auth L]241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IML3MCM19YBR107CYBR0836
UniProt
Find proteins for P38265 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38265 
Go to UniProtKB:  P38265
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit CHL4H [auth N]447Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CHL4CTF17MCM17YDR254WYD9320A.04
UniProt
Find proteins for P38907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38907 
Go to UniProtKB:  P38907
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit MCM21I [auth O]212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM21CTF5YDR318W
UniProt
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06675 
Go to UniProtKB:  Q06675
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit CTF19J [auth P]270Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF19MCM18YPL018WLPB13W
UniProt
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02732 
Go to UniProtKB:  Q02732
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit OKP1K [auth Q]231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OKP1YGR179C
UniProt
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53298 
Go to UniProtKB:  P53298
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit AME1L [auth U]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AME1ARP100YBR211CYBR1458
UniProt
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38313 
Go to UniProtKB:  P38313
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP1M [auth Y]237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NKP1YDR383C
UniProt
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12493 
Go to UniProtKB:  Q12493
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Inner kinetochore subunit NKP2N [auth Z]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NKP2YLR315W
UniProt
Find proteins for Q06162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06162 
Go to UniProtKB:  Q06162
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein CSE4O [auth a]90Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSE4CSL2YKL049CYKL262
UniProt
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36012 
Go to UniProtKB:  P36012
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4P [auth b], S [auth f]79Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02309 
Go to UniProtKB:  P02309
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.2Q [auth d]93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB2H2B2YBL002WYBL0104
UniProt
Find proteins for P02294 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02294 
Go to UniProtKB:  P02294
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3-like centromeric protein CSE4R [auth e]115Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSE4CSL2YKL049CYKL262
UniProt
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36012 
Go to UniProtKB:  P36012
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.1T [auth g]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04911 
Go to UniProtKB:  P04911
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B.1U [auth h]94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02293 
Go to UniProtKB:  P02293
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A.1V [auth i]102Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04911 
Go to UniProtKB:  P04911
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (125-MER)B [auth G]124Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (125-MER)E [auth J]124Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




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