PDBsum entry 5b0y

DNA binding protein

PDB id: 5b0y

Contents

Protein chains

96 a.a.

78 a.a.

105 a.a.

93 a.a.

84 a.a.

DNA/RNA

Metals

_CL ×2

_MN ×8

Waters ×32

PDB id:

5b0y

Name:

DNA binding protein

Title:

Crystal structure of the nucleosome containing histone h3 with the crotonylated lysine 122

Structure:

Histone h3.2. Chain: a, e. Synonym: histone h3/m,histone h3/o. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a type 1-b/e. Chain: c, g.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hist2h3a, hist2h3c, h3f2, h3fm, hist2h3d. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g, h4fg, hist1h4d, h4/b, h4fb, hist1h4e, h4/j, h4fj, hist1h4f, h4/c, h4fc, hist1h4h, h4/h, h4fh, hist1h4i, h4/m, h4fm, hist1h4j, h4/e,

Resolution:

2.56Å R-factor: 0.212 R-free: 0.249

Authors:

Y.Suzuki,N.Horikoshi,H.Kurumizaka

Key ref:

Y.Suzuki et al. (2016). Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122. Biochem Biophys Res Commun, 469, 483-489. PubMed id: 26694698 DOI: 10.1016/j.bbrc.2015.12.041

Date:

13-Nov-15 Release date: 27-Jan-16

Protein chains

Q71DI3  (H32_HUMAN) -  Histone H3.2 from Homo sapiens

Seq: 136 a.a.

Struc: 96 a.a.*

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens

Seq: 130 a.a.

Struc: 105 a.a.

Protein chains

P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J from Homo sapiens

Seq: 126 a.a.

Struc: 93 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 84 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1016/j.bbrc.2015.12.041

Biochem Biophys Res Commun 469:483-489 (2016)

PubMed id: 26694698

Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122.

Y.Suzuki, N.Horikoshi, D.Kato, H.Kurumizaka.

ABSTRACT

The crotonylation of histones is an important post-translational modification, and epigenetically functions in the regulation of genomic DNA activity. The histone modifications in the structured "histone-fold" domains are considered to have an especially important impact on the nucleosome structure and dynamics. In the present study, we reconstituted the human nucleosome containing histone H3.2 crotonylated at the Lys122 residue, and determined its crystal structure at 2.56 Å resolution. We found that the crotonylation of the H3 Lys122 residue does not affect the overall nucleosome structure, but locally impedes the formation of the water-mediated hydrogen bond with the DNA backbone. Consistently, thermal stability assays revealed that the H3 Lys122 crotonylation, as well as the H3 Lys122 acetylation, clearly reduced the histone-DNA association.