7TQV

SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA

Summary for 7TQV

• Entry DOI: 10.2210/pdb7tqv/pdb
• EMDB information: 25915 26073
• Descriptor: Uridylate-specific endoribonuclease, RNA (33-MER) (3 entities in total)
• Functional Keywords: endoribonuclease, viral protein, viral protein-rna complex, viral protein/rna
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 8
• Total formula weight: 277493.41

Authors

Frazier, M.N.,Krahn, J.M.,Butay, K.J.,Dillard, L.B.,Borgnia, M.J.,Stanley, R.E. (deposition date: 2022-01-27, release date: 2022-03-23, Last modification date: 2024-06-12)

Primary citation

Frazier, M.N.,Wilson, I.M.,Krahn, J.M.,Butay, K.J.,Dillard, L.B.,Borgnia, M.J.,Stanley, R.E.
Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.
Nucleic Acids Res., 50:8290-8301, 2022

PubMed 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.

PubMed: 35801916
DOI: 10.1093/nar/gkac589

Experimental method

ELECTRON MICROSCOPY (3.43 Å)