PDBsum entry 3x1s

Structural protein/DNA

PDB id: 3x1s

Contents

Protein chains

96 a.a.

78 a.a.

105 a.a.

94 a.a.

84 a.a.

DNA/RNA

Metals

_MN ×6

_CL ×2

Waters ×11

PDB id:

3x1s

Name:

Structural protein/DNA

Title:

Crystal structure of the nucleosome core particle

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: h2a, h3fa, h3fb, h3fc, h3fd, h3ff, h3fh, h3fi, h3fj, h3fk, h3fl, hist1h3a, hist1h3b, hist1h3c, hist1h3d, hist1h3e, hist1h3f, hist1h3g, hist1h3h, hist1h3i, hist1h3j. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: h2b, h4/a, h4/b, h4/c, h4/d, h4/e, h4/g, h4/h, h4/i, h4/j,

Resolution:

2.81Å R-factor: 0.224 R-free: 0.270

Authors:

P.Sivaraman,T.S.Kumarevel

Key ref:

S.Padavattan et al. (2015). Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming. Biochem Biophys Res Commun, 464, 929-935. PubMed id: 26188507 DOI: 10.1016/j.bbrc.2015.07.070

Date:

27-Nov-14 Release date: 23-Sep-15

Protein chains

P68431  (H31_HUMAN) -  Histone H3.1 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

P33778  (H2B1B_HUMAN) -  Histone H2B type 1-B from Homo sapiens

Seq: 126 a.a.

Struc: 94 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- 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.2015.07.070

Biochem Biophys Res Commun 464:929-935 (2015)

PubMed id: 26188507

Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming.

S.Padavattan, T.Shinagawa, K.Hasegawa, T.Kumasaka, S.Ishii, T.Kumarevel.

ABSTRACT

Histone variants TH2a and TH2b are highly expressed in testes, oocytes and zygotes. Our recent analysis suggested that these histone variants enhance the induced generation of pluripotent stem cells (iPSCs) when co-expressed along with four transcription factors, Oct3/4, Sox2, Klf4 and c-Myc (OSKM), and are associated with an open chromatin structure [1]. In the present study, we report the crystal structures of nucleosomes (NCPs) with the mouse histone variants, TH2a and TH2b. The structures revealed two significant changes, as compared to the canonical counterparts: fewer histone-DNA contacts and changes in dimer-dimer interactions between TH2a-TH2a' (L1-loop). In vivo studies with domain swapping and point mutants of the variants revealed that the residues in the histone tails and the TH2a-L1 loop are important for reprogramming. Taken together, our work indicates that the NCP variants with structural modifications and flexible tails are most likely important for enhanced reprogramming of functions.