PDBsum entry 5b2i

Transcription/DNA

PDB id: 5b2i

Contents

Protein chains

99 a.a.

82 a.a.

106 a.a.

97 a.a.

DNA/RNA

Metals

_MN ×4

PDB id:

5b2i

Name:

Transcription/DNA

Title:

Human nucleosome containing cpg unmethylated DNA

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: hist1h3a, h3fa, hist1h3b, h3fl, hist1h3c, h3fc, hist1h3d, h3fb, hist1h3e, h3fd, hist1h3f, h3fi, hist1h3g, h3fh, hist1h3h, h3fk, hist1h3i, h3ff, hist1h3j, h3fj. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768. Gene: hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g,

Resolution:

3.00Å R-factor: 0.203 R-free: 0.257

Authors:

Y.Fujii,M.Wakamori,T.Umehara,S.Yokoyama

Key ref:

Y.Fujii et al. (2016). Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation. FEBS Open Bio, 6, 498-514. PubMed id: 27419055 DOI: 10.1002/2211-5463.12064

Date:

16-Jan-16 Release date: 15-Jun-16

Protein chains

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

Seq: 136 a.a.

Struc: 99 a.a.

Protein chains

P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens

Seq: 103 a.a.

Struc: 82 a.a.

Protein chains

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

Seq: 130 a.a.

Struc: 106 a.a.

Protein chains

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

Seq: 126 a.a.

Struc: 97 a.a.

DNA/RNA chains

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

DOI no: 10.1002/2211-5463.12064

FEBS Open Bio 6:498-514 (2016)

PubMed id: 27419055

Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation.

Y.Fujii, M.Wakamori, T.Umehara, S.Yokoyama.

ABSTRACT

Cytosine methylation, predominantly of the CpG sequence in vertebrates, is one of the major epigenetic modifications crucially involved in the control of gene expression. Due to the difficulty of reconstituting site-specifically methylated nucleosomal DNA at crystallization quality, most structural analyses of CpG methylation have been performed using chemically synthesized oligonucleotides, There has been just one recent study of nucleosome core particles (NCPs) reconstituted with nonpalindromic human satellite 2-derived DNAs. Through the preparation of a 146-bp palindromic α-satellite-based nucleosomal DNA containing four CpG dinucleotide sequences and its enzymatic methylation and restriction, we reconstituted a 'symmetric' human CpG-methylated nucleosome core particle (NCP). We solved the crystal structures of the CpG-methylated and unmodified NCPs at 2.6 and 3.0 Å resolution, respectively. We observed the electron densities of two methyl groups, among the eight 5-methylcytosines introduced in the CpG-fully methylated NCP. There were no obvious structural differences between the CpG-methylated 'symmetric NCP' and the unmodified NCP. The preparation of a crystallization-grade CpG-methylated NCP provides a platform for the analysis of CpG-methyl reader and eraser proteins.