Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A7B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 202.25 kDa 
• Atom Count: 11920 
• Residue Count: 1042 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

5XM1

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4

• DOI: 10.2210/pdb5XM1/pdb
• NDB: 5XM1

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli, Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2017-05-12 Released: 2018-03-07 
• Deposition Author(s): Taguchi, H., Horikoshi, N., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science, Ministry of Education, Culture, Sports, Science and Technology, the Japan Agency for Medical Research and Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 

Literature

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.

Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H., Ohkawa, Y.

(2018) Nat Commun 9: 1400-1400

• PubMed: 29643389 
• DOI: 10.1038/s41467-018-03845-1
• Primary Citation of Related Structures:  
  5XM1, 5XM0


• PubMed Abstract: 
  

Regulation of gene expression requires selective incorporation of histone H3 variant H3.3 into chromatin. Histone H3.3 has several subsidiary variants but their functions are unclear. Here we characterize the function of histone H3.3 sub-variant, H3mm7, which is expressed in skeletal muscle satellite cells. H3mm7 knockout mice demonstrate an essential role of H3mm7 in skeletal muscle regeneration. Chromatin analysis reveals that H3mm7 facilitates transcription by forming an open chromatin structure around promoter regions including those of myogenic genes. The crystal structure of the nucleosome containing H3mm7 reveals that, unlike the S57 residue of other H3 proteins, the H3mm7-specific A57 residue cannot form a hydrogen bond with the R40 residue of the cognate H4 molecule. Consequently, the H3mm7 nucleosome is unstable in vitro and exhibited higher mobility in vivo compared with the H3.3 nucleosome. We conclude that the unstable H3mm7 nucleosome may be required for proper skeletal muscle differentiation.

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Organizational Affiliation: 

Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3mm7	A, E	139	Mus musculus	Mutation(s): 0  Gene Names: H3-3a, H3.3a, H3f3a, H3-3b, H3.3b, H3f3b
Find proteins for P84244 (Mus musculus) Explore P84244  Go to UniProtKB:  P84244

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, H4c1, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4c11, H4c12, H4c14, H4f16
Find proteins for P62806 (Mus musculus) Explore P62806  Go to UniProtKB:  P62806
NIH Common Fund Data Resources
IMPC  MGI: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, H2ac4
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
Find proteins for Q9D2U9 (Mus musculus) Explore Q9D2U9  Go to UniProtKB:  Q9D2U9

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I, J	146	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.55	α = 90
b = 109.38	β = 90
c = 176.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-12 
• Released Date: 2018-03-07 
Deposition Author(s): Taguchi, H., Horikoshi, N., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--
Ministry of Education, Culture, Sports, Science and Technology	Japan	25116002
the Japan Agency for Medical Research and Development	Japan	--

Revision History 

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references