Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 10-mer - A8B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 348.16 kDa 
• Atom Count: 12,693 
• Modelled Residue Count: 1,154 
• Deposited Residue Count: 2,616 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

 7BY0

The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C

• PDB DOI: 10.2210/pdb7BY0/pdb
• EM Map EMD-30239: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Gallus gallus, Homo sapiens, synthetic construct, unidentified cloning vector
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-21 Released: 2021-02-10 
• Deposition Author(s): Ariyoshi, M., Makino, F., Fukagawa, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 33463726 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2,Histone H3-like centromeric protein A	A, E	141	Gallus gallus	Mutation(s): 0  Gene Names: CENPA
UniProt
Find proteins for Q6XXM1 (Gallus gallus) Explore Q6XXM1  Go to UniProtKB:  Q6XXM1
Find proteins for P84229 (Gallus gallus) Explore P84229  Go to UniProtKB:  P84229
UniProt Groups	Q6XXM1P84229

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	130	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	126	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H2BJ, H2BFR, H2BC11
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose Binding Protein tag, linker,CENP-C	K, L	664	unidentified cloning vector, Gallus gallus This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for O57393 (Gallus gallus) Explore O57393  Go to UniProtKB:  O57393
UniProt Groups	O57393P0AEX9

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	145	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	K, L	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.08

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Ariyoshi, M., Makino, F., Fukagawa, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	25221106
Japan Agency for Medical Research and Development (AMED)	Japan	0101117
Japan Agency for Medical Research and Development (AMED)	Japan	0101020

Revision History  

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