5XM1 image
Deposition Date 2017-05-12
Release Date 2018-03-07
Last Version Date 2023-11-22
Entry Detail
PDB ID:
5XM1
Title:
The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.45 Å
R-Value Free:
0.25
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Histone H3mm7
Chain IDs:A, E
Chain Length:139
Number of Molecules:2
Biological Source:Mus musculus
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
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B
Gene (Uniprot):H2ac4
Chain IDs:C, G
Chain Length:133
Number of Molecules:2
Biological Source:Mus musculus
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
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:I, J
Chain Length:146
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.
Nat Commun 9 1400 1400 (2018)
PMID: 29643389 DOI: 10.1038/s41467-018-03845-1

Abstact

Regulation of gene expression requires selective incorporation of histone H3 variant H3.3 into chromatin. Histone H3.3 has several subsidiary variants but their functions are unclear. Here we characterize the function of histone H3.3 sub-variant, H3mm7, which is expressed in skeletal muscle satellite cells. H3mm7 knockout mice demonstrate an essential role of H3mm7 in skeletal muscle regeneration. Chromatin analysis reveals that H3mm7 facilitates transcription by forming an open chromatin structure around promoter regions including those of myogenic genes. The crystal structure of the nucleosome containing H3mm7 reveals that, unlike the S57 residue of other H3 proteins, the H3mm7-specific A57 residue cannot form a hydrogen bond with the R40 residue of the cognate H4 molecule. Consequently, the H3mm7 nucleosome is unstable in vitro and exhibited higher mobility in vivo compared with the H3.3 nucleosome. We conclude that the unstable H3mm7 nucleosome may be required for proper skeletal muscle differentiation.

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Primary Citation of related structures