9MB2 | pdb_00009mb2

The mouse nucleosome structure containing H3mm15

• PDB DOI: https://doi.org/10.2210/pdb9MB2/pdb
• EM Map EMD-63765: EMDB EMDataResource

• Classification: NUCLEAR PROTEIN/DNA
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-15 Released: 2026-09-09 
• Deposition Author(s): Ho, C.-H., Kurumizaka, H.
• Funding Organization(s): Japan Science and Technology, Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Histone H3.3 subvariant H3mm15 is required for normal spermatogenesis by regulating gene expression

Wu, Q., Harada, A., Ho, C.-H., Tanaka, K., Maehara, K., Shimada, R., Ishiguro, K., Oki, S., Kurumizaka, H., Takemoto, T., Ohkawa, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A6B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 201.3 kDa 
• Atom Count: 11,916 
• Modeled Residue Count: 1,045 
• Deposited Residue Count: 1,302 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3mm15	A, E	138	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Mus musculus	Mutation(s): 0  Gene Names:  Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus) Explore P62806  Go to UniProtKB:  P62806
IMPC:  MGI:2448419MGI:2448420MGI:2448443

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B	C, G	133	Mus musculus	Mutation(s): 0  Gene Names: Hist1h2ab
UniProt
Find proteins for C0HKE1 (Mus musculus) Explore C0HKE1  Go to UniProtKB:  C0HKE1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 3-A	D, H	129	Mus musculus	Mutation(s): 0  Gene Names: Hist3h2ba
UniProt
Find proteins for Q9D2U9 (Mus musculus) Explore Q9D2U9  Go to UniProtKB:  Q9D2U9

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Ho, C.-H., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR24T3
Japan Science and Technology	Japan	JPMJER1901
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121009
Japan Society for the Promotion of Science (JSPS)	Japan	JP23H05475
Japan Society for the Promotion of Science (JSPS)	Japan	JP24H02328

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release