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TitleStructural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 6521, Year 2025
Publish dateJul 15, 2025
AuthorsSara Landeras-Bueno / Chitra Hariharan / Ruben Diaz Avalos / Andrew S Norris / Dalton T Snyder / Kathryn M Hastie / Stephanie Harkins / Michelle Zandonatti / Roshan R Rajamanickam / Eduardo Olmedillas / Robyn Miller / Sujan Shresta / Vicki H Wysocki / Erica Ollmann Saphire /
PubMed AbstractThe nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. ...The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N hampers its structural analysis. Here, we describe a stepwise method using viral-derived RNAs to stabilize SARS-CoV-2 N for EM analysis. We identify pieces of RNA from the SARS-CoV-2 genome that promote the formation of structurally homogeneous N dimers, intermediates of assembly, and filamentous capsid-like structures. Building on these results, we engineer a symmetric RNA to stabilize N protein dimers, the building block of high-order assemblies, for EM studies. We combine domain-specific monoclonal antibodies against N with chemical cross-linking mass spectrometry to validate the spatial arrangement of the N domains within the dimer. Additionally, our cryo-EM analysis reveals novel antigenic sites on the N protein. Our findings provide insights into N protein´s architectural and antigenic principles, which can guide design of pan-coronavirus therapeutics.
External linksNat Commun / PubMed:40664703 / PubMed Central
MethodsEM (single particle)
Resolution3.7 - 8.24 Å
Structure data

45157

9c2h

EMDB-45157, PDB-9c2h:
SARS-CoV-2 Nucleocapsid Dimerization Domain bound to Fab-NP1E9 and Fab-NP3B4
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-45158: SARS-CoV-2 Nucleocapsid dimer complexed to 24 bp RNA
Method: EM (single particle) / Resolution: 8.24 Å

Source
  • severe acute respiratory syndrome coronavirus 2
  • mus sp. (mice)
  • synthetic RNA (others)
KeywordsVIRAL PROTEIN / Protein / Fab / immunocomplex

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