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TitleCryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 636, Year 2021
Publish dateJan 27, 2021
AuthorsMonica C Pillon / Meredith N Frazier / Lucas B Dillard / Jason G Williams / Seda Kocaman / Juno M Krahn / Lalith Perera / Cassandra K Hayne / Jacob Gordon / Zachary D Stewart / Mack Sobhany / Leesa J Deterding / Allen L Hsu / Venkata P Dandey / Mario J Borgnia / Robin E Stanley /
PubMed AbstractNsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses ...Nsp15, a uridine specific endoribonuclease conserved across coronaviruses, processes viral RNA to evade detection by host defense systems. Crystal structures of Nsp15 from different coronaviruses have shown a common hexameric assembly, yet how the enzyme recognizes and processes RNA remains poorly understood. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15, in both apo and UTP-bound states. The cryo-EM reconstructions, combined with biochemistry, mass spectrometry, and molecular dynamics, expose molecular details of how critical active site residues recognize uridine and facilitate catalysis of the phosphodiester bond. Mass spectrometry revealed the accumulation of cyclic phosphate cleavage products, while analysis of the apo and UTP-bound datasets revealed conformational dynamics not observed by crystal structures that are likely important to facilitate substrate recognition and regulate nuclease activity. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.
External linksNat Commun / PubMed:33504779 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.3 Å
Structure data

EMDB-22610, PDB-7k0r:
Nucleotide bound SARS-CoV-2 Nsp15
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-22611:
SARS-CoV-2 wt-Nsp15 APO-state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-22612:
SARS-CoV-2 Nsp15 H235A variant APO-state, dataset ii
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-22613:
SARS-CoV-2 Nsp15 H235A APO-state, dataset i
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-U5P:
URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate

ChemComp-PO4:
PHOSPHATE ION / Phosphate

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Ribonuclease

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