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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/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. 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3t
A, E
139Mus musculusMutation(s): 0 
Gene Names: Gm12260
UniProt
Find proteins for P68433 (Mus musculus)
Explore P68433 
Go to UniProtKB:  P68433
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UniProt GroupP68433
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Mus 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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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
133Mus musculusMutation(s): 0 
Gene Names: Hist1h2abHist1h2acHist1h2adHist1h2aeHist1h2agHist1h2aiHist1h2anHist1h2ao
UniProt
Find proteins for C0HKE1 (Mus musculus)
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UniProt GroupC0HKE1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 3-A
D, H
129Mus musculusMutation(s): 0 
Gene Names: Hist3h2ba
UniProt
Find proteins for Q9D2U9 (Mus musculus)
Explore Q9D2U9 
Go to UniProtKB:  Q9D2U9
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UniProt GroupQ9D2U9
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
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
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

View Full Validation Report



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
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description