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: