Spike of variant has a slightly different amino acids (PDB ID:7dwx, 7k8z, 7l2d)


Many variants of the coronavirus are reported, such as "alpha" and "delta" variants. These variants are characterized by the mutation of amino acids in the spike proteins. The mutations are often called as the combination of wild type amino acid, residue number and mutated amino acid, such as "N501Y" and "P681H". For example, "N501Y" means Asparagine (N) in the 501-th site is mutated into Tyrosine (Y). The following buttons, such as "N501Y" and "P681H", correspond to the mutation site. If you click one of these buttons, for example "N501Y", the corresponding site (the 501-th amino acid) is displayed as "red balls". Note that three sites are always displayed as red balls, because the spike is composed of the three identical chains. Because the 501-th site is in the interface with the human ACE2 receptor, the mutation N501Y can change the binding ability of the spike to the ACE2. It can also affect the binding to antibodies. Similarly, the mutation T478K can affect the binding to ACE2 and antibodies.

In contrast, the site P681 is very far from the interfaces of ACE2 and antibodies, the mutations P681H and P681R can not directly affect the binding. However, please remember again that the cleavage of S1/S2 is necessary for the membrane fusion. Clicking thu button "S1/S2 cleavage sites(685/686)" shows the cleavage sites as "green balls". The site P681 is close to the cleavage sites, the mutation in the P681 may affect the cleavage of S1/S2 and enhance infectivity.
See the " 20 amino acids in proteins" for one-letter descriptions of 20 amino acids, such as "N" and "Y".

Spike S1/S2 cleavage site(685/686) human ACE2 receptor antibodies virus membrane
Alpha variant N501Y P681H
Delta variant T19R G142D L452R T478K D614G P681R D950N
Turn Stop