7R98

Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6

Replaces:  7N0S

Summary for 7R98

• Entry DOI: 10.2210/pdb7r98/pdb
• Descriptor: Nucleoprotein, Nanobody B6 (2 entities in total)
• Functional Keywords: sars-cov-2, nanobody, nucleocapsid, virus, viral protein-immune system complex, rna binding protein, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 6
• Total formula weight: 86928.52

Authors

Corbett, K.D.,Ye, Q. (deposition date: 2021-06-28, release date: 2021-07-07, Last modification date: 2024-10-09)

Primary citation

Ye, Q.,Lu, S.,Corbett, K.D.
Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies.
Front Immunol, 12:719037-719037, 2021

PubMed Abstract: The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.

PubMed: 34381460
DOI: 10.3389/fimmu.2021.719037

Experimental method

X-RAY DIFFRACTION (2.51 Å)