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

• Published in: Nature communications Vol. 14; no. 1; p. 1955
• Main Authors: Das, Naba K., Hollmann, Nele M., Vogt, Jeff, Sevdalis, Spiridon E., Banna, Hasan A., Ojha, Manju, Koirala, Deepak
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07.04.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 101/1; 631/326/596/2148; 631/45/500; 631/535/1266; 82/1; 82/16; 82/80; 82/83; Antibodies; Crystal structure; Domains; Enteroviruses; Genomes; Helices; Humanities and Social Sciences; multidisciplinary; NMR; Nuclear magnetic resonance; Nucleic Acid Conformation; Phylogeny; Poliovirus - genetics; Protein Binding; Proteins; Replication; Ribonucleic acid; RNA; RNA - metabolism; RNA Replication; RNA, Viral - metabolism; Science; Science & Technology - Other Topics; Science (multidisciplinary); Virus Replication
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-37658-8

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. A cloverleaf-like RNA domain within the enterovirus genome is essential for replication. Here, the authors determine the 1.9 Å resolution crystal structure of such RNA from coxsackievirus B3 – a model enterovirus to study many other human viruses.