Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

0536797 - ÚOCHB 2021 RIV US eng J - Journal Article
Dinesh, Dhurvas Chandrasekaran - Chalupská, Dominika - Šilhán, Jan - Koutná, Eliška - Nencka, Radim - Veverka, Václav - Bouřa, Evžen
Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.
PLoS Pathogens. Roč. 16, č. 12 (2020), č. článku e1009100. ISSN 1553-7366. E-ISSN 1553-7374
R&D Projects: GA MŠMT(CZ) EF16_019/0000729
Grant - others:AV ČR(CZ) L200551951
Institutional support: RVO:61388963
Keywords : N-terminal domain * binding domain * crystal structure
OECD category: Biochemistry and molecular biology
Impact factor: 6.823, year: 2020
Method of publishing: Open access
https://doi.org/10.1371/journal.ppat.1009100

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positivesense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.
Permanent Link: http://hdl.handle.net/11104/0316257