Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer - A6B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 203.32 kDa 
• Atom Count: 12164 
• Residue Count: 1043 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

5B1L

The mouse nucleosome structure containing H3t

• DOI: 10.2210/pdb5B1L/pdb
• NDB: 5B1L

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli, Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2015-12-08 Released: 2017-02-15 
• Deposition Author(s): Urahama, T., Machida, S., Horikoshi, N., Osakabe, A., Tachiwana, H., Taguchi, H., Kurumizaka, H.
• Funding Organization(s): the Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (MEXT)

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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 

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

• PubMed: 28099840 
• 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 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3t	A, E	139	Mus musculus	Mutation(s): 0  Gene Names:  Gm12260, H3c1, H3a, Hist1h3a, H3c8, H3.1-221, H3g, Hist1h3g, H3c10, H3.1-291, H3h, Hist1h3h, H3c11, H3.1-I, H3i, Hist1h3i
Find proteins for P68433 (Mus musculus) Explore P68433  Go to UniProtKB:  P68433

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Mus musculus	Mutation(s): 0  Gene Names:  Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4, H4c1, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4c11, H4c12, H4c14, H4f16
Find proteins for P62806 (Mus musculus) Explore P62806  Go to UniProtKB:  P62806
NIH Common Fund Data Resources
IMPC  MGI:2448443

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	133	Mus musculus	Mutation(s): 0  Gene Names: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag, Hist1h2ai, Hist1h2an, Hist1h2ao, H2ac4
Find proteins for C0HKE1 (Mus musculus) Explore C0HKE1  Go to UniProtKB:  C0HKE1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 3-A	D, H	129	Mus musculus	Mutation(s): 0  Gene Names: Hist3h2ba
Find proteins for Q9D2U9 (Mus musculus) Explore Q9D2U9  Go to UniProtKB:  Q9D2U9

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (146-MER)	I, J	146	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D, I, J	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	A, C, E, 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 = 98.968	α = 90
b = 107.425	β = 90
c = 167.332	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-12-08 
• Released Date: 2017-02-15 
Deposition Author(s): Urahama, T., Machida, S., Horikoshi, N., Osakabe, A., Tachiwana, H., Taguchi, H., Kurumizaka, H.

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Funding Organization	Location	Grant Number
the Japan Agency for Medical Research and Development (AMED)	Japan	--
Ministry of Education, Culture, Sports, Science and Technology (MEXT)	Japan	25116002

Revision History 

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