5B2J

Human nucleosome containing CpG methylated DNA

5B2J の概要

• エントリーDOI: 10.2210/pdb5b2j/pdb
• 関連するPDBエントリー: 5B2I
• 分子名称: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (7 entities in total)
• 機能のキーワード: chromatin, epigenetics, histone, transcription, transcription-dna complex, transcription/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 202725.49

構造登録者

Fujii, Y.,Wakamori, M.,Umehara, T.,Yokoyama, S. (登録日: 2016-01-18, 公開日: 2016-06-15, 最終更新日: 2023-11-08)

主引用文献

Fujii, Y.,Wakamori, M.,Umehara, T.,Yokoyama, S.
Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation.
Febs Open Bio, 6:498-514, 2016

PubMed 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.

PubMed: 27419055
DOI: 10.1002/2211-5463.12064

実験手法

X-RAY DIFFRACTION (2.6 Å)