Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease

Nucleic Acids Res. 2022 Aug 12;50(14):8290-8301. doi: 10.1093/nar/gkac589.


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.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • COVID-19*
  • Endoribonucleases* / metabolism
  • Humans
  • RNA, Double-Stranded / genetics
  • SARS-CoV-2 / genetics
  • Uridine
  • Viral Nonstructural Proteins / metabolism


  • RNA, Double-Stranded
  • Viral Nonstructural Proteins
  • Endoribonucleases
  • Uridine