Molecule of the Month: SARS-CoV-2 Nucleocapsid and Home Tests
Home test kits for SARS-CoV-2 test for the presence of nucleocapsid, the protein that packages the viral genome in infectious virions.
Testing at Home
Order and Disorder
Exploring the Structure
Nucleocapsid uses several structural tricks to bind tightly to RNA. First, the RNA-binding domain has a long loop that bends down and grips the RNA. Second, this loop and the groove that it forms are lined with arginine and lysine amino acids (shown in purple and turquoise here), which are positively-charged and interact favorably with the negatively-charged RNA. To explore the three-dimensional aspects of this interaction, click on the image for an interactive JSmol that includes the RNA-bound structure (7act) and the protein alone (6yi3).
Topics for Further Discussion
- Superimposed coordinates for the antibody illustration and JSmol were created by overlapping the structures using the Pairwise Structure Alignment tool at the RCSB PDB website. Try the alignment of RNA-binding domains, and use the SelectView-->Structures menu to view the RNA.
- You can get an overview of all the structures of nucleocapsid using the Group Sequence page at the RCSB PDB website. Notice there are a few structures that include the central linker region.
Related PDB-101 Resources
- Browse Coronavirus
- Browse Viruses
- Browse You and Your Health
- Browse Immune System
- Frank, F., Keen, M.M., Rao, A., Bassit, L., Liu, L., Liu, X., Bowers, H.B., Patel, A.B., Cato, M.L., Sullivan, J.A., Greenleaf, M., Piantadosi, A., Lam, W.A., Hudson, W.H., Orlund, E.A. (2020) Deep mutational scanning identifies SARS-CoV-2 nucleocapsid escape mutations of currently available rapid antigen tests. Cell 185: 3603-3616
- 6yi3, 7act: Dinesh, D.C., Chalupska, D., Silhan, J., Koutna, E., Nencka, R., Veverka, V., Boura, E. (2020) Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein. PLoS Pathog 16: e1009100
- Peng, Y., Du, N., Lei, Y., Dorje, S., Qi, J., Luo, T., Gao, G.F., Song, H. (2020) Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design. EMBO J 39: e105938
February 2023, David Goodselldoi:10.2210/rcsb_pdb/mom_2023_2