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: https://doi.org/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. 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

    Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3,Histone H3-like centromeric protein A
A, E
144Gallus gallusMutation(s): 0 
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UniProt GroupsP84229Q6XXM1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-E
D, H
129Homo sapiensMutation(s): 0 
Gene Names: H2BC21H2BFQHIST2H2BE
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GTEx:  ENSG00000184678 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CENP-C
K, L
41Gallus gallusMutation(s): 0 
UniProt
Find proteins for O57392 (Gallus gallus)
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UniProt GroupO57392
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Centromere protein N
M, N
630unidentified cloning vectorGallus gallus
This entity is chimeric
Mutation(s): 0 
UniProt
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Find proteins for P0AEX9 (Escherichia coli (strain K12))
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UniProt GroupsQ1T765P0AEX9
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-mer)145synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-mer)145synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.08

Structure Validation

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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