7K0R

Nucleotide bound SARS-CoV-2 Nsp15

Summary for 7K0R

• Entry DOI: 10.2210/pdb7k0r/pdb
• EMDB information: 22610
• Descriptor: Uridylate-specific endoribonuclease, URIDINE-5'-MONOPHOSPHATE, PHOSPHATE ION (3 entities in total)
• Functional Keywords: ribonuclease, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV)
• Total number of polymer chains: 6
• Total formula weight: 247100.93

Authors

Pillon, M.C.,Stanley, R.E. (deposition date: 2020-09-04, release date: 2020-12-09, Last modification date: 2024-03-06)

Primary citation

Pillon, M.C.,Frazier, M.N.,Dillard, L.B.,Williams, J.G.,Kocaman, S.,Krahn, J.M.,Perera, L.,Hayne, C.K.,Gordon, J.,Stewart, Z.D.,Sobhany, M.,Deterding, L.J.,Hsu, A.L.,Dandey, V.P.,Borgnia, M.J.,Stanley, R.E.
Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.
Nat Commun, 12:636-636, 2021

PubMed Abstract: 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.

PubMed: 33504779
DOI: 10.1038/s41467-020-20608-z

Experimental method

ELECTRON MICROSCOPY (3.3 Å)