8DP3

Crystal structure of coxsackievirus B3 cloverleaf RNA replication element

Summary for 8DP3

• Entry DOI: 10.2210/pdb8dp3/pdb
• Descriptor: Fab BL3-6 Heavy Chain, Fab BL3-6 Light Chain, RNA (90-MER), ... (5 entities in total)
• Functional Keywords: rna, fab, enteroviral replication, immune system-rna complex, immune system/rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 3
• Total formula weight: 82089.60

Authors

Das, N.K.,Koirala, D. (deposition date: 2022-07-14, release date: 2023-04-19, Last modification date: 2024-10-30)

Primary citation

Das, N.K.,Hollmann, N.M.,Vogt, J.,Sevdalis, S.E.,Banna, H.A.,Ojha, M.,Koirala, D.
Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element.
Nat Commun, 14:1955-1955, 2023

PubMed 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.

PubMed: 37029118
DOI: 10.1038/s41467-023-37658-8

Experimental method

X-RAY DIFFRACTION (1.91 Å)