7SZU

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6

7SZU の概要

• エントリーDOI: 10.2210/pdb7szu/pdb
• 分子名称: RNA aptamer, BL3-6 Fab heavy chain, BL3-6 Fab light chain, ... (7 entities in total)
• 機能のキーワード: fluorogenic, immune system-rna complex, immune system/rna
• 由来する生物種: Mus musculus (Mouse); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 69063.95

構造登録者

Rees, H.C.,Piccirilli, J.A. (登録日: 2021-11-29, 公開日: 2022-07-06, 最終更新日: 2024-11-20)

主引用文献

Rees, H.C.,Gogacz, W.,Li, N.S.,Koirala, D.,Piccirilli, J.A.
Structural Basis for Fluorescence Activation by Pepper RNA.
Acs Chem.Biol., 17:1866-1875, 2022

PubMed Abstract: Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 Å resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple·base-triple stack to sandwich the ligand with a U·G wobble pair. Site-bound Mg ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.

PubMed: 35759696
DOI: 10.1021/acschembio.2c00290

実験手法

X-RAY DIFFRACTION (2.24 Å)