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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5B1L, 5B1M

  • 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 stages of spermatogenesis ...

    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 H3tA, E139Mus musculusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P68433 (Mus musculus)
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Go to UniProtKB:  P68433
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UniProt GroupP68433
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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 1C, G133Mus musculusMutation(s): 0 
Gene Names: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao, H2ac4
UniProt
Find proteins for C0HKE1 (Mus musculus)
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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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download Ideal Coordinates CCD File 
AA [auth J],
M [auth D],
P [auth I],
Q [auth I],
R [auth I],
AA [auth J],
M [auth D],
P [auth I],
Q [auth I],
R [auth I],
S [auth I],
T [auth I],
U [auth I],
V [auth J],
W [auth J],
X [auth J],
Y [auth J],
Z [auth J]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
K [auth A],
L [auth C],
N [auth E],
O [auth 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 
  • 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  (Full details and data files)

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