SNAP output for PDB entry 7tqv [SNAP web server]

PDB-id

7tqv; SNAP-derived features in text and JSON formats; DNAproDB

Class

viral protein-RNA

Method

cryo-EM (3.43 Å)

Summary

Sars-cov-2 endoribonuclease nsp15 bound to dsrna

Reference

Frazier MN, Wilson IM, Krahn JM, Butay KJ, Dillard LB, Borgnia MJ, Stanley RE (2022): "Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease." Nucleic Acids Res., 50, 8290-8301. doi: 10.1093/nar/gkac589.

Abstract

Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.