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

Naba K. Das, Nele M. Hollmann, Jeff Vogt, Spiridon E. Sevdalis, Hasan A. Banna, Manju Ojha and Deepak Koirala ()
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Naba K. Das: University of Maryland Baltimore County
Nele M. Hollmann: University of Maryland Baltimore County
Jeff Vogt: University of Maryland Baltimore County
Spiridon E. Sevdalis: University of Maryland School of Medicine
Hasan A. Banna: University of Maryland Baltimore County
Manju Ojha: University of Maryland Baltimore County
Deepak Koirala: University of Maryland Baltimore County

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-37658-8

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