Cryo-EM data analysis and visualization
Single-particle cryo-EM data analysis of BG505 SOSIP.664 in complex with RM20A3 Fab was reproduced directly from Berndsen et al.51. Data for the SARS-CoV S 2P ectodomain was previously published52 and the final particle stack and alignment parameters from the published reconstruction were used for 3D variability analysis in the SPARX software package76,77. All metadata for these reconstructions along with raw data images and FSC resolution curves can be found in the original publications. In summary, both datasets were acquired on a FEI Titan Krios (Thermo Fisher) operating at 300 KeV equipped with a K2 Summit Direct Electron Detector (Gatan). Movie micrographs were aligned and dose weighted with MotionCor278 and CTF estimation was performed with Gctf79. Single-particle data processing was performed using CryoSparc v.280 and Relion v.381. Maps were low-pass filtered using a Gaussian kernel and visualized in UCSF chimera82. A detailed description of the auto-thresholding method used to set the isosurface value for visualisation of low-pass filtered maps can be found in Berndsen et al.51.