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:  

  • 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 <sup>1,2 </sup>, function to co ...

    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.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Humboldt-Universität zu Berlin, Institut für Biologie, Berlin, Germany.,MRC Laboratory of Molecular Biology, Cambridge, UK. dbarford@mrc-lmb.cam.ac.uk.,Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit MIF2
C
22Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MIF2
Find proteins for P35201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35201
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit MCM16
H
133Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM16
Find proteins for Q12262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12262
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit CTF3
I
408Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CTF3 (CHL3)
Find proteins for Q12748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12748
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit MCM22
K
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM22
Find proteins for P47167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47167
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit IML3
L
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IML3 (MCM19)
Find proteins for P38265 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38265
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit CHL4
N
447Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CHL4 (CTF17, MCM17)
Find proteins for P38907 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38907
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit MCM21
O
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM21 (CTF5)
Find proteins for Q06675 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06675
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit CTF19
P
270Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CTF19 (MCM18)
Find proteins for Q02732 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02732
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit OKP1
Q
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: OKP1
Find proteins for P53298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53298
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit AME1
U
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: AME1 (ARP100)
Find proteins for P38313 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38313
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit NKP1
Y
237Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NKP1
Find proteins for Q12493 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12493
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Inner kinetochore subunit NKP2
Z
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NKP2
Find proteins for Q06162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06162
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein CSE4
a
90Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSE4 (CSL2)
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36012
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Histone H4
b, f
79Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHF1, HHF2
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02309
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.2
d
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTB2 (H2B2)
Find proteins for P02294 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02294
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Histone H3-like centromeric protein CSE4
e
115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSE4 (CSL2)
Find proteins for P36012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36012
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1
g
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTA1 (H2A1, SPT11)
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04911
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Histone H2B.1
h
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTB1 (H2B1, SPT12)
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02293
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Histone H2A.1
i
102Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTA1 (H2A1, SPT11)
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04911
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (125-MER)G124Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (125-MER)J124Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Database references