8YV8

Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence.

• PDB DOI: https://doi.org/10.2210/pdb8YV8/pdb
• EM Map EMD-39594: EMDB EMDataResource
• NAKB: 8YV8

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-28 Released: 2024-07-31 
• Deposition Author(s): Kikuchi, A., Shikimachi, R., Nishiyama, A., Funabiki, H., Arita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS

Wassing, I., Nishiyama, A., Arita, K., Funabiki, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 210.86 kDa 
• Atom Count: 12,248 
• Modelled Residue Count: 1,125 
• Deposited Residue Count: 1,380 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	135	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	129	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 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D, H	125	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814 GTEx:  ENSG00000197903

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division cycle-associated protein 7	K	108	Homo sapiens	Mutation(s): 1  Gene Names: CDCA7, JPO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWT1 (Homo sapiens) Explore Q9BWT1  Go to UniProtKB:  Q9BWT1
PHAROS:  Q9BWT1 GTEx:  ENSG00000144354

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (132-MER)	I	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (132-MER)	J	145	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	L [auth K], M [auth K], N [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Kikuchi, A., Shikimachi, R., Nishiyama, A., Funabiki, H., Arita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H05740, JP19H03143, JP19H05285, JP19H05741
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35GM132111, R35GM133780

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release