5T3K

Fluorescence detection of RNA-ligand binding and crystal structure determination of ribosomal decoding site RNA using a heavy atom containing fluorescent ribonucleoside

5T3K の概要

• エントリーDOI: 10.2210/pdb5t3k/pdb
• 分子名称: RNA (5'-R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*GP*G)-3'), RNA (5'-R(*CP*AP*GP*CP*GP*(75B)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3'), MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: bacterial decoding site rna, rna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 21641.91

構造登録者

Hermann, T.,Boerneke, M.A. (登録日: 2016-08-25, 公開日: 2017-07-05, 最終更新日: 2024-03-06)

主引用文献

Nuthanakanti, A.,Boerneke, M.A.,Hermann, T.,Srivatsan, S.G.
Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.
Angew. Chem. Int. Ed. Engl., 56:2640-2644, 2017

PubMed Abstract: Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation-sensitive fluorophore and an anomalous X-ray diffraction label (5-selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand-induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.

PubMed: 28156044
DOI: 10.1002/anie.201611700

実験手法

X-RAY DIFFRACTION (2.142 Å)