A presumed RNA cloverleaf (5′CL), located at the 5′-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem–loop B (SLB) and stem–loop D (SLD), the two largest stem–loops within the 5′CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5′CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB and SLD into close contact, a geometry that creates an extensive accessible major groove surface, and permits interaction between the proteins that target each stem–loop.
© 2019 Warden et al.; Published by Cold Spring Harbor Laboratory Press for the RNA society. This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) License.
Original Publication Citation
Warden, M. S., Cai, K., Cornilescu, G., Burke, J. E., Ponniah, K., Butcher, S. E., & Pascal, S. M. (2019). Conformational flexibility in the enterovirus RNA replication platform. RNA, 25(3), 376-387. https://doi.org/10.1261/rna.069476.118
Warden, Meghan S.; Cai, Kai; Cornilescu, Gabriel; Burke, Jordan E.; Ponniah, Komala; Butcher, Samuel E.; and Pascal, Steven M., "Conformational Flexibility in the Enterovirus RNA Replication Platform" (2019). Chemistry & Biochemistry Faculty Publications. 271.