Molecule of the Month: SARS-CoV-2 Spike

The research community has quickly mobilized to fight the current SARS-CoV-2 pandemic, building on years of work on the previous SARS-CoV virus. The spike protein of this virus will be a central figure in this fight, since it is the primary target of antibodies that provide immunity against the virus. The surfaces of coronaviruses are covered with these spikes, giving them their distinctive crown-like appearance in electron micrographs. The spikes initiate the process of infection, binding to receptors and then fusing with the cell membrane to release the viral genome inside. Many other enveloped viruses use similar spike-like proteins to infect cells, including influenza hemagglutinin, and the envelope glycoproteins of HIV-1 and ebola.

The spike protein is composed of three identical chains, that together form a complex with a small domain inside the virus, a membrane-spanning segment, and a large ectodomain that extends outward from the virus. In addition, the spike is a glycoprotein: the ectodomain is covered with sugar chains that help to mask the virus from the immune system. The structures of SARS-CoV and SARS-COV-2 spikes shown here (PDB entries 6crz and 6vxx) include only the ectodomain, and as you can see, they are very similar. Each chain is synthesized in one piece, but then is clipped by cellular proteases into two functional pieces. The outer S1 fragment, colored magenta, binds to cellular receptors, and the S2 fragment, colored red, directs fusion of the virus with the cell. Both of these structures include only portions of the many sugar chains that coat the spike, since the sugars are highly flexible and difficult to observe.

Recent structures have revealed that the spikes of SARS-CoV and SARS-CoV-2 are quite flexible. In these structures, the receptor-binding domains are seen in different conformations. Often, just one domain is extended upwards, but sometimes they're all tucked down or several are extended. The extended conformation is needed to bind to receptors, so this flexibility is a great advantage to the virus. Researchers hypothesize that the recent SARS variants are virulent because their receptor binding domains are particularly flexible, whereas the more widespread coronaviruses that cause the common cold are less dangerous because they are less flexible.

Spike protein binds to ACE2 (angiotensin-converting enzyme 2) on the surface of cells. ACE2 is an enzyme that activates angiotensin, a peptide hormone involved in control of blood pressure. ACE2 is found on lung, heart, kidney, and intestinal cells, making these cells the target for infection by the virus. PDB entry 6m17 reveals the complex of ACE2 with the receptor-binding domain of the SARS-CoV-2 spike. In the complex, ACE2 is also bound to the amino acid transporter B0AT1. The illustration was created by superimposing this complex with the structure of the spike protein in PDB entry 6vsb.