7BXT

The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C.

Ariyoshi, M.Makino, F.Watanabe, R.Nakagawa, R.Kato, T.Namba, K.Arimura, Y.Fujita, R.Kurumizaka, H.Okumura, E.I.Hara, M.Fukagawa, T.

(2021) EMBO J 40: e105671-e105671

  • DOI: 10.15252/embj.2020105671
  • Primary Citation of Related Structures:  
    7BXT, 7BY0

  • PubMed Abstract: 
  • The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a kinetochore. CENP-C and CENP-N are CENP-A binding proteins. We previously demonstrated that vertebrate CENP-C binding to the CENP-A nucleosome is regulated by CDK1-mediated CENP-C phosphorylation ...

    The CENP-A nucleosome is a key structure for kinetochore assembly. Once the CENP-A nucleosome is established in the centromere, additional proteins recognize the CENP-A nucleosome to form a kinetochore. CENP-C and CENP-N are CENP-A binding proteins. We previously demonstrated that vertebrate CENP-C binding to the CENP-A nucleosome is regulated by CDK1-mediated CENP-C phosphorylation. However, it is still unknown how the phosphorylation of CENP-C regulates its binding to CENP-A. It is also not completely understood how and whether CENP-C and CENP-N act together on the CENP-A nucleosome. Here, using cryo-electron microscopy (cryo-EM) in combination with biochemical approaches, we reveal a stable CENP-A nucleosome-binding mode of CENP-C through unique regions. The chicken CENP-C structure bound to the CENP-A nucleosome is stabilized by an intramolecular link through the phosphorylated CENP-C residue. The stable CENP-A-CENP-C complex excludes CENP-N from the CENP-A nucleosome. These findings provide mechanistic insights into the dynamic kinetochore assembly regulated by CDK1-mediated CENP-C phosphorylation.


    Organizational Affiliation

    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3,Histone H3-like centromeric protein AA, E144Gallus gallusMutation(s): 0 
Gene Names: CENPA
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UniProt GroupsQ6XXM1P84229
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 2-ED, H129Homo sapiensMutation(s): 0 
Gene Names: H2BC21H2BFQHIST2H2BE
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Find proteins for Q16778 (Homo sapiens)
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GTEx:  ENSG00000184678 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
CENP-CK, L41Gallus gallusMutation(s): 0 
Gene Names: CENPC
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Centromere protein NM, N630unidentified cloning vectorGallus gallus
This entity is chimeric
Mutation(s): 0 
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Find proteins for Q1T765 (Gallus gallus)
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Find proteins for P0AEX9 (Escherichia coli (strain K12))
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UniProt GroupsP0AEX9Q1T765
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Entity ID: 5
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DNA (145-mer)I 145synthetic construct
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Entity ID: 6
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DNA (145-mer)J 145synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan25221106
Japan Agency for Medical Research and Development (AMED)Japan0101117
Japan Agency for Medical Research and Development (AMED)Japan0101020

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references