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DOE OSTI · 2423332

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

Das, Naba K.·Hollmann, Nele M.·Vogt, Jeff·Sevdalis, Spiridon E.·Banna, Hasan A.·Ojha, Manju·Koirala, Deepak
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Abstract

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

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Das, Naba K., Hollmann, Nele M., Vogt, Jeff, Sevdalis, Spiridon E., Banna, Hasan A., Ojha, Manju, Koirala, Deepak. 2023-04-07. Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. https://doi.org/10.1038/s41467-023-37658-8

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