9CJ6

Crystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex with ssDNA.

Summary for 9CJ6

• Entry DOI: 10.2210/pdb9cj6/pdb
• Descriptor: Nucleoprotein, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') (3 entities in total)
• Functional Keywords: structural protein, viral protein, nucleocapsid, protein-dna complex, viral protein-dna complex, viral protein/dna
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 2
• Total formula weight: 51728.54

Authors

Maiti, A.,Matsuo, H. (deposition date: 2024-07-05, release date: 2024-12-11, Last modification date: 2025-01-22)

Primary citation

Maiti, A.,Matsuo, H.
Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.
Biomolecules, 14:-, 2024

PubMed Abstract: 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 by which the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, targeting the N protein has several advantages: it exhibits 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 developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55 Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure revealed new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identified residues that are critical for ssDNA interaction.

PubMed: 39766245
DOI: 10.3390/biom14121538

Experimental method

X-RAY DIFFRACTION (1.55 Å)