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 

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:  

  • 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, H3m ...

    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.,Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Yokohama, 226-8503, Japan.,Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan. yohkawa@bioreg.kyushu-u.ac.jp.,Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Research Institute for Science and Engineering, and Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3mm7
A, E
139Mus musculusMutation(s): 0 
Gene Names: H3f3a, H3f3b (H3.3a, H3.3b)
Find proteins for P84244 (Mus musculus)
Go to UniProtKB:  P84244
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Mus musculusMutation(s): 0 
Gene Names: Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist4h4 (H4-53, H4-12, Hist2h4)
Find proteins for P62806 (Mus musculus)
Go to UniProtKB:  P62806
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B
C, G
133Mus musculusMutation(s): 0 
Gene Names: Hist1h2ab
Find proteins for C0HKE1 (Mus musculus)
Go to UniProtKB:  C0HKE1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 3-A
D, H
129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus)
Go to UniProtKB:  Q9D2U9
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (146-MER)I,J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.550α = 90.00
b = 109.380β = 90.00
c = 176.209γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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