1S32

Molecular Recognition of the Nucleosomal 'Supergroove'

1S32 の概要

• エントリーDOI: 10.2210/pdb1s32/pdb
• 関連するPDBエントリー: 1AOI 1KX3 1KX5 1M18 1M19 1M1A
• 分子名称: palindromic alpha-satellite 146 bp DNA fragment, BETA-ALANINE, 3-AMINO-(DIMETHYLPROPYLAMINE), ... (14 entities in total)
• 機能のキーワード: nucleosome core particle (ncp), pyrrole-imidazole (py-im) hairpin polyamide, clamp, nucleosome dynamics, structural protein-dna complex, structural protein/dna
• 由来する生物種: Xenopus laevis (African clawed frog); 詳細
• 細胞内の位置: Nucleus: A0A310TTQ1
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 200097.79

構造登録者

Edayathumangalam, R.S.,Weyermann, P.,Gottesfeld, J.M.,Dervan, P.B.,Luger, K. (登録日: 2004-01-12, 公開日: 2004-05-11, 最終更新日: 2023-11-15)

主引用文献

Edayathumangalam, R.S.,Weyermann, P.,Gottesfeld, J.M.,Dervan, P.B.,Luger, K.
Molecular Recognition of the Nucleosomal 'Supergroove'
Proc.Natl.Acad.Sci.USA, 101:6864-6869, 2004

PubMed Abstract: Chromatin is the physiological substrate in all processes involving eukaryotic DNA. By organizing 147 base pairs of DNA into two tight superhelical coils, the nucleosome generates an architecture where DNA regions that are 80 base pairs apart on linear DNA are brought into close proximity, resulting in the formation of DNA "supergrooves." Here, we report the design of a hairpin polyamide dimer that targets one such supergroove. The 2-A crystal structure of the nucleosome-polyamide complex shows that the bivalent "clamp" effectively crosslinks the two gyres of the DNA superhelix, improves positioning of the DNA on the histone octamer, and stabilizes the nucleosome against dissociation. Our findings identify nucleosomal supergrooves as platforms for molecular recognition of condensed eukaryotic DNA. In vivo, supergrooves may foster synergistic protein-protein interactions by bringing two regulatory elements into juxtaposition. Because supergroove formation is independent of the translational position of the DNA on the histone octamer, accurate nucleosome positioning over regulatory elements is not required for supergroove participation in eukaryotic gene regulation.

PubMed: 15100411
DOI: 10.1073/pnas.0401743101

実験手法

X-RAY DIFFRACTION (2.05 Å)