2.5 Model building and visualization
Initial model building of the different conformations of mink S glycoprotein and the mvACE2 complex was performed in UCSF ChimeraX using PDB 6ACJ and 7LWI for global mink S-mvACE2 complex and PDB 7F5R for mink S glycoprotein RBD-mvACE2 complex after local refinement as a starting model. Several rounds of refinement in Phenix and manual building in Coot were performed until the final reliable models were obtained. Model and map statistics are summarized in Supplementary Tables 1-2.
Figures were generated using UCSF ChimeraX and PyMol. UCSF ChimeraX was used to measure the angles between the RBD and spike protein33. The ”Define” function was used to generate the horizontal plane of the American mink S glycoprotein and long axis across the RBD. The ”angle” function was used to calculate the angles between the plane and the axis.
Cryo-EM reconstructions and atomic models generated in this study are available at the Protein Data Base (PDB) under the following accession codes: mink S glycoprotein alone (8T21), mink S glycoprotein bound to one mvACE2 with downRBD (8T22) or upRBD (8TAZ), mink S glycoprotein bound to two mvACE2 (8T20), and local refinement of the RBD-ACE2 interface of downRBD (8T25) and upRBD (8T23).
3. Results: