5XM1

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

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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    Organizational Affiliation: 

    Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan. yohkawa@bioreg.kyushu-u.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3mm7A, E139Mus musculusMutation(s): 0 
Gene Names: H3-3a, H3.3a, H3f3a, H3-3b, H3.3b, H3f3b
UniProt
Find proteins for P84244 (Mus musculus)
Explore P84244 
Go to UniProtKB:  P84244
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UniProt GroupP84244
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F106Mus musculusMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62806 (Mus musculus)
Explore P62806 
Go to UniProtKB:  P62806
IMPC:  MGI:2448443
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UniProt GroupP62806
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-BC, G133Mus musculusMutation(s): 0 
Gene Names: Hist1h2ab, H2ac4
UniProt
Find proteins for C0HKE1 (Mus musculus)
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Go to UniProtKB:  C0HKE1
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UniProt GroupC0HKE1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 3-AD, H129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba, H2bu2
UniProt
Find proteins for Q9D2U9 (Mus musculus)
Explore Q9D2U9 
Go to UniProtKB:  Q9D2U9
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UniProt GroupQ9D2U9
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J 146Homo sapiens
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  • Reference Sequence
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 = 105.55α = 90
b = 109.38β = 90
c = 176.209γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKLdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--
Ministry of Education, Culture, Sports, Science and TechnologyJapan25116002
the Japan Agency for Medical Research and DevelopmentJapan--

Revision History  (Full details and data files)

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