9BIH
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA with 1 nucleotide bulge
Summary for 9BIH
| Entry DOI | 10.2210/pdb9bih/pdb |
| EMDB information | 44590 |
| Descriptor | Uridylate-specific endoribonuclease nsp15, RNA (35-mer), RNA (34-mer) (3 entities in total) |
| Functional Keywords | uridine-specific endonuclease, bulged dsrna, unpaired nucleotide, coronavirus, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 More |
| Total number of polymer chains | 8 |
| Total formula weight | 257434.13 |
| Authors | Wright, Z.M.,Butay, K.J.,Krahn, J.M.,Borgnia, M.J.,Stanley, R.E. (deposition date: 2024-04-23, release date: 2024-12-18, Last modification date: 2025-01-15) |
| Primary citation | Wright, Z.M.,Butay, K.J.,Krahn, J.M.,Wilson, I.M.,Gabel, S.A.,DeRose, E.F.,Hissein, I.S.,Williams, J.G.,Borgnia, M.J.,Frazier, M.N.,Mueller, G.A.,Stanley, R.E. Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates. Nat Commun, 16:391-391, 2025 Cited by PubMed Abstract: Coronaviruses evade detection by the host immune system with the help of the endoribonuclease Nsp15, which regulates levels of viral double stranded RNA by cleaving 3' of uridine (U). While prior structural data shows that to cleave double stranded RNA, Nsp15's target U must be flipped out of the helix, it is not yet understood whether Nsp15 initiates flipping or captures spontaneously flipped bases. We address this gap by designing fluorinated double stranded RNA substrates that allow us to directly relate a U's sequence context to both its tendency to spontaneously flip and its susceptibility to cleavage by Nsp15. Through a combination of nuclease assays, F NMR spectroscopy, mass spectrometry, and single particle cryo-EM, we determine that Nsp15 acts most efficiently on unpaired Us, particularly those that are already flipped. Across sequence contexts, we find Nsp15's cleavage efficiency to be directly related to that U's tendency to spontaneously flip. Overall, our findings unify previous characterizations of Nsp15's cleavage preferences, and suggest that activity of Nsp15 during infection is partially driven by bulged or otherwise relatively accessible Us that appear at strategic positions in the viral RNA. PubMed: 39755678DOI: 10.1038/s41467-024-55682-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.24 Å) |
Structure validation
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