3.4 Structure of SARS-CoV-2 S glycoprotein trimer with upRBD
bound to mvACE2 receptor
One of the three mvACE2-bound spike trimers captured had a strong
density for mvACE2 bound to two of the RBD at 69.2°. After multiple
rounds of additional 2D and 3D classification analysis, we determined
the complex structure of mink S glycoprotein bound to two mvACE2 at 3.36
Å (Fig. 5A, S1B, and S1D). The local resolution of the protein interface
between the complex was low due to its flexibility in the region.
Nonetheless, the overall architecture of the mvACE2-mink S glycoprotein
complex was comparable to the previously published structure. To
visualize the key interaction at the protein interface between the
complex, we performed local refinement with the mask covering the
RBD-ACE2 interface, returning the improved resolution of the density map
at 3.82Å (Fig. 5B, S1G, and S1I). To analyze the binding interface
between the complex, we selected residues located less than 4.0 Å
apart40 (Fig 5C).
Overall, our structure largely agreed with the previous Y453F RBD-mink
ACE2 in interface residues8,9 (Fig. 5D-F). Notable
interactions include a salt bridge between mink S D405 with mvACE2 H354
and S E484 with mvACE2 H79; hydrogen bond between S T500 with mvACE2
Y41, S G502 with mvACE2 K353, and S Y505 with mvACE2 R393; π-cation
interaction between S Y489 with mvACE2 K31; and π-π stacking between S
F453 with mvACE2 Y34 and S Y505 with mvACE2 H354. F453 in S glycoprotein
is unique to the mink variant among other S variants (Fig. 3), and as
indicated in our structural and binding affinity studies, as well as
noted in previous studies8,9, Y453F mink S
glycoprotein enhances the interaction with mvACE2 Y34.