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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

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:  

  • 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: 

    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo 162-8480, Japan.,Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan.,Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan.,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.,Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan.,Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan; Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan. Electronic address: junueda@isc.chubu.ac.jp.,Research and Development Center, Fuso Pharmaceutical Industries, Ltd., Osaka 536-8523, Japan; Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3t
A, E
139Mus musculusMutation(s): 0 
Gene Names: H3c1, H3c8, H3c10, H3c11 (H3a, Hist1h3a, H3.1-221, H3g, Hist1h3g, H3.1-291, H3h, Hist1h3h, H3.1-I, H3i, Hist1h3i)
Find proteins for P68433 (Mus musculus)
Go to UniProtKB:  P68433
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
106Mus musculusMutation(s): 0 
Gene Names: H4c1, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4c11, H4c12, Hist1h4m, H4c14, H4f16 (Hist1h4a, H4-53, Hist1h4b, H4-12, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist2h4, Hist2h4a, Hist4h4)
Find proteins for P62806 (Mus musculus)
Go to UniProtKB:  P62806
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
C, G
133Mus musculusMutation(s): 0 
Gene Names: H2ac4 (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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
D, I, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, C, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.968α = 90.00
b = 107.425β = 90.00
c = 167.332γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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