PDBsum entry 5xm0

Structural protein/DNA

PDB id: 5xm0

Contents

Protein chains

97 a.a.

78 a.a.

105 a.a.

94 a.a.

84 a.a.

DNA/RNA

Waters ×12

PDB id:

5xm0

Name:

Structural protein/DNA

Title:

The mouse nucleosome structure containing h2a, h2b type3-a, h3.3, and h4

Structure:

Histone h3.3. Chain: a, e. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a type 1-b. Chain: c, g. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: h3f3a, h3.3a, h3f3b, h3.3b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: hist1h4a, hist1h4b, h4-53, hist1h4c, h4-12, hist1h4d, hist1h4f, hist1h4h, hist1h4i, hist1h4j, hist1h4k, hist1h4m, hist2h4a, hist2h4, hist4h4.

Resolution:

2.87Å R-factor: 0.221 R-free: 0.255

Authors:

H.Taguchi,N.Horikoshi,H.Kurumizaka

Key ref:

A.Harada et al. (2018). Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Nat Commun, 9, 1400. PubMed id: 29643389 DOI: 10.1038/s41467-018-03845-1

Date:

12-May-17 Release date: 07-Mar-18

Protein chains

P84244  (H33_MOUSE) -  Histone H3.3 from Mus musculus

Seq: 136 a.a.

Struc: 97 a.a.

Protein chain

P62806  (H4_MOUSE) -  Histone H4 from Mus musculus

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

C0HKE1  (H2A1B_MOUSE) -  Histone H2A type 1-B from Mus musculus

Seq: 130 a.a.

Struc: 105 a.a.

Protein chains

Q9D2U9  (H2B3A_MOUSE) -  H2B.U histone 2 from Mus musculus

Seq: 126 a.a.

Struc: 94 a.a.

Protein chain

P62806  (H4_MOUSE) -  Histone H4 from Mus musculus

Seq: 103 a.a.

Struc: 84 a.a.

DNA/RNA chains

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 146 bases

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-T-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 146 bases

DOI no: 10.1038/s41467-018-03845-1

Nat Commun 9:1400 (2018)

PubMed id: 29643389

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.

A.Harada, K.Maehara, Y.Ono, H.Taguchi, K.Yoshioka, Y.Kitajima, Y.Xie, Y.Sato, T.Iwasaki, J.Nogami, S.Okada, T.Komatsu, Y.Semba, T.Takemoto, H.Kimura, H.Kurumizaka, Y.Ohkawa.

ABSTRACT

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.