7EOK

Crystal structure of the Pepper aptamer in complex with HBC485

7EOK の概要

• エントリーDOI: 10.2210/pdb7eok/pdb
• 分子名称: Pepper (49-MER), GUANOSINE-5'-TRIPHOSPHATE, 4-[(~{Z})-1-cyano-2-[5-[2-(dimethylamino)ethyl-methyl-amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile, ... (5 entities in total)
• 機能のキーワード: fluorescent rna, aptamer, hbc485, rna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16502.49

構造登録者

Huang, K.Y.,Ren, A.M. (登録日: 2021-04-22, 公開日: 2021-11-24, 最終更新日: 2023-11-29)

主引用文献

Huang, K.,Chen, X.,Li, C.,Song, Q.,Li, H.,Zhu, L.,Yang, Y.,Ren, A.
Structure-based investigation of fluorogenic Pepper aptamer.
Nat.Chem.Biol., 17:1289-1295, 2021

PubMed Abstract: Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G·U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization.

PubMed: 34725509
DOI: 10.1038/s41589-021-00884-6

実験手法

X-RAY DIFFRACTION (2.7 Å)