Fig. 4: Parsing of complex native environments and accurate identification of membrane-bound complexes.
From: MiLoPYP: self-supervised molecular pattern mining and particle localization in situ
We analyzed tilt series from EMPIAR-10453 containing SARS-CoV-2 viruses with spike protein attached to their surfaces. a, 2D grid visualization of SARS-CoV-2 sample showing patches corresponding to free-floating and membrane-bound spikes (top, left). 3D tomogram visualization with voxels colored according to the embedding coordinate values (top, right). Selections of patches containing free-floating spikes (purple outline) and membrane-attached spikes are shown below (pink outline). b, Membrane-attached SARS-CoV-2 spike localization after running the refinement module (pink circles). c, 5.6 Å and 9.3 Å resolution structures for the open and closed states determined by SPT from a total of 13,047 spikes extracted from 266 tomograms: open state reconstructed from 9,194 particles (left), and closed state from 3,740 particles (right). PDB coordinates 6VYB and 6VXX were fitted into the maps using rigid body fitting, respectively.
