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TitleFlipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.
Journal, issue, pagesNucleic Acids Res, Vol. 50, Issue 14, Page 8290-8301, Year 2022
Publish dateAug 12, 2022
AuthorsMeredith N Frazier / Isha M Wilson / Juno M Krahn / Kevin John Butay / Lucas B Dillard / Mario J Borgnia / Robin E Stanley
PubMed AbstractCoronaviruses 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 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.
External linksNucleic Acids Res / PubMed:35801916 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.43 Å
Structure data

25915

7tj2

EMDB-25915, PDB-7tj2:
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA
Method: EM (single particle) / Resolution: 3.2 Å

26073

7tqv

EMDB-26073, PDB-7tqv:
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA
Method: EM (single particle) / Resolution: 3.43 Å

Source
  • severe acute respiratory syndrome coronavirus 2
  • synthetic construct (others)
  • unidentified (others)
KeywordsVIRAL PROTEIN/RNA / endoribonuclease / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex

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