5B1L

The mouse nucleosome structure containing H3t


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis

Ueda, J.Harada, A.Urahama, T.Machida, S.Maehara, K.Hada, M.Makino, Y.Nogami, J.Horikoshi, N.Osakabe, A.Taguchi, H.Tanaka, H.Tachiwana, H.Yao, T.Yamada, M.Iwamoto, T.Isotani, A.Ikawa, M.Tachibana, T.Okada, Y.Kimura, H.Ohkawa, Y.Kurumizaka, H.Yamagata, K.

(2017) Cell Rep 18: 593-600

  • DOI: 10.1016/j.celrep.2016.12.065
  • Primary Citation of Related Structures:  
    5B1M, 5B1L

  • PubMed Abstract: 
  • Cellular differentiation is associated with dynamic chromatin remodeling in establishing a cell-type-specific epigenomic landscape. Here, we find that mouse testis-specific and replication-dependent histone H3 variant H3t is essential for very early ...

    Cellular differentiation is associated with dynamic chromatin remodeling in establishing a cell-type-specific epigenomic landscape. Here, we find that mouse testis-specific and replication-dependent histone H3 variant H3t is essential for very early stages of spermatogenesis. H3t gene deficiency leads to azoospermia because of the loss of haploid germ cells. When differentiating spermatogonia emerge in normal spermatogenesis, H3t appears and replaces the canonical H3 proteins. Structural and biochemical analyses reveal that H3t-containing nucleosomes are more flexible than the canonical nucleosomes. Thus, by incorporating H3t into the genome during spermatogonial differentiation, male germ cells are able to enter meiosis and beyond.


    Organizational Affiliation

    Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan; Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan. Electronic address: yamagata@waka.kindai.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3tAE139Mus musculusMutation(s): 0 
Gene Names: 
Find proteins for P68433 (Mus musculus)
Explore P68433 
Go to UniProtKB:  P68433
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF106Mus musculusMutation(s): 0 
Gene Names: 
Find proteins for P62806 (Mus musculus)
Explore P62806 
Go to UniProtKB:  P62806
NIH Common Fund Data Resources
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1CG133Mus musculusMutation(s): 0 
Gene Names: Hist1h2abHist1h2acHist1h2adHist1h2aeHist1h2agHist1h2aiHist1h2anHist1h2aoH2ac4
Find proteins for C0HKE1 (Mus musculus)
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Go to UniProtKB:  C0HKE1
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 3-ADH129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus)
Explore Q9D2U9 
Go to UniProtKB:  Q9D2U9
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)I, J146Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.968α = 90
b = 107.425β = 90
c = 167.332γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Japan Agency for Medical Research and Development (AMED)Japan--
Ministry of Education, Culture, Sports, Science and Technology (MEXT)Japan25116002

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection