Affinity tag free purification of SARS-Cov-2 N protein and its crystal structure in complex with ssDNA

The nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms of how the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, the N protein has several advantages: higher sequence conservation, lower mutation rates, and stronger immunogenicity, making it an attractive target for antiviral drug development and diagnostics. Therefore, a detailed understanding of the N protein’s structure is essential for deciphering its role in viral assembly and for developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure reveals new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identify residues that are critical for ssDNA interaction.