PDBsum entry 3wkj

Structural protein/DNA

PDB id: 3wkj

Contents

Protein chains

97 a.a.

78 a.a.

107 a.a.

93 a.a.

84 a.a.

DNA/RNA

Metals

_CL ×4

_MN ×5

Waters ×101

PDB id:

3wkj

Name:

Structural protein/DNA

Title:

The nucleosome containing human tsh2b

Structure:

Histone h3.1. Chain: a, e. Synonym: histone h3/a, histone h3/b, histone h3/c, histone h3/d, histone h3/f, histone h3/h, histone h3/i, histone h3/j, histone h3/k, histone h3/l. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: h3.1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: h4. Gene: h2a. Gene: hist1h2ba, tsh2b.

Resolution:

2.80Å R-factor: 0.235 R-free: 0.291

Authors:

T.Urahama,N.Horikoshi,A.Osakabe,H.Tachiwana,H.Kurumizaka

Key ref:

T.Urahama et al. (2014). Structure of human nucleosome containing the testis-specific histone variant TSH2B. Acta Crystallogr F Struct Biol Commun, 70, 444-449. PubMed id: 24699735 DOI: 10.1107/S2053230X14004695

Date:

22-Oct-13 Release date: 09-Apr-14

Protein chains

P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens

Seq: 136 a.a.

Struc: 97 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: 107 a.a.

Protein chains

Q96A08  (H2B1A_HUMAN) -  Histone H2B type 1-A from Homo sapiens

Seq: 127 a.a.

Struc: 93 a.a.

Protein chain

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

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- 145 bases

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-G- 145 bases

DOI no: 10.1107/S2053230X14004695

Acta Crystallogr F Struct Biol Commun 70:444-449 (2014)

PubMed id: 24699735

Structure of human nucleosome containing the testis-specific histone variant TSH2B.

T.Urahama, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Kurumizaka.

ABSTRACT

The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with the H4 Arg78 residue. In contrast, the other TSH2B-specific amino-acid residues did not induce any significant local structural changes in the TSH2B nucleosome. These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis.