5T3K

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

Summary for 5T3K

• Entry DOI: 10.2210/pdb5t3k/pdb
• Descriptor: 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)
• Functional Keywords: bacterial decoding site rna, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 4
• Total formula weight: 21641.91

Authors

Hermann, T.,Boerneke, M.A. (deposition date: 2016-08-25, release date: 2017-07-05, Last modification date: 2024-03-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.142 Å)