ISDA

Deposition Date 2015-12-08

Release Date 2017-02-15

Last Version Date 2023-11-08

Entry Detail

PDB ID:

5B1M

Keywords:

STRUCTURAL PROTEIN/DNA

Title:

The mouse nucleosome structure containing H3.1

Biological Source:

Source Organism:

Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.34 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3c1, H3c8, H3c10, H3c11
Chain IDs:A, E
Chain Length:139
Number of Molecules:2
Biological Source:Mus musculus

UniProt ID:P68433 Pfam ID:PF00125

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4c1, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4c11, H4c12, Hist1h4m, H4c14, H4c16
Chain IDs:B, F
Chain Length:106
Number of Molecules:2
Biological Source:Mus musculus

UniProt ID:P62806 Pfam ID:PF15511

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:C, G
Chain Length:133
Number of Molecules:2
Biological Source:Mus musculus

UniProt ID:C0HKE1 Pfam ID:PF00125, PF16211

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B type 3-A
Gene (Uniprot):H2bu2
Chain IDs:D, H
Chain Length:129
Number of Molecules:2
Biological Source:Mus musculus

UniProt ID:Q9D2U9 Pfam ID:PF00125

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:I, J
Chain Length:146
Number of Molecules:2
Biological Source:Homo sapiens

Primary Citation

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.Show

Cell Rep 18 593 600 (2017)

PMID: 28099840 DOI: 10.1016/j.celrep.2016.12.065

Abstact

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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