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.

A dimer of SARS-CoV-2 nucleocapsid. Structurally-ordered domains are depicted from the atomic structures and disordered regions are shown schematically. Nucleocapsid is in magenta and purple, and short RNA strands are in yellow.
A dimer of SARS-CoV-2 nucleocapsid. Structurally-ordered domains are depicted from the atomic structures and disordered regions are shown schematically. Nucleocapsid is in magenta and purple, and short RNA strands are in yellow.
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Soon after the COVID19 pandemic began, the research community mobilized to find ways to fight it. Thanks to these efforts, we have many effective methods for stopping the spread of the virus. Vaccines protect us against infection and nirmatrelvir (the anti-viral active ingredient in Pfizer's Paxlovid) can be used to help treat people who get infected. But perhaps most importantly, many easy-to-use home test kits are widely available to see if we are infected. This is a central tool in the fight against SARS-CoV-2, since it allows us to test ourselves any time and quarantine if we’re infected, thus giving us greater confidence in the safety of social situations.

Testing at Home

Most home test kits look for the presence of nucleocapsid in the sample that we collect. Nucleocapsid has the job of packaging the viral genome inside virions. It is made in large quantities in cells infected by SARS-CoV-2, so it provides an effective target for testing. The tests typically use a “flow-through” technology. A small sample is placed in a small well and the molecules flow through an area that has antibodies that recognize nucleocapsid. Then the antibody-bound nucleocapsid flows further and is captured in the distinctive line of a positive test. These tests also include a control that tests for a common molecule, such as our own antibodies, just to make sure the sample was collected correctly.

Order and Disorder

Nucleocapsid is a complex molecule with many functional parts. One section folds into an RNA-binding domain (PDB ID 7act), with a groove that grips a short segment of the viral genomic RNA. Another section folds into a dimerization domain (6wji) that brings two nucleocapsid molecules together. The rest of the protein is intrinsically disordered, forming tails at each end of the protein chain and a flexible linker that connects the two structured domains. These disordered regions assist with RNA binding and orchestrate association of nucleocapsid dimers into larger assemblies that package the DNA in the small space inside virions.

Three structures of antibodies (blue) bound to different faces of SARS-CoV-2 nucleocapsid (magenta).
Three structures of antibodies (blue) bound to different faces of SARS-CoV-2 nucleocapsid (magenta).
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Antibody Recognition

SARS-CoV-2 home test kits rely on antibodies that specifically recognize nucleocapsid within the complex mix of biomolecules found in a nasal sample. Different brands of these kits use different antibodies that recognize different portions of the molecule. This is not surprising, since the immune system is very effective at developing antibodies that probe all aspects of a target molecule, so developers of tests have many choices for the antibodies they use. For example, the illustration shown here superimposes three structures of antibodies bound to different faces of the RNA-binding domain of nucleocapsid, from PDB ID 7cr5, 7n3c, and 7sts.

Exploring the Structure

RNA-Binding Domain

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

  1. 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.
  2. 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.

References

  1. 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
  2. 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
  3. 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 Goodsell

doi:10.2210/rcsb_pdb/mom_2023_2
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More
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