Figure 5: TomoDRGN captures intermolecular heterogeneity in situ.

(a) UMAP of tomoDRGN latent embeddings of particles (n=20,981) re-extracted with box size ~3x particle radius. Colored volumes sampled from correspondingly colored points in UMAP are shown.

(b) Violin plot of the distance from each particle in the indicated classes from panel (a) to its nearest neighbor ribosome. Distribution colors are paired with those in (a). The right bound of the x-axis corresponds to the box diameter, and the red interval on the x-axis corresponds to typical inter-ribosome distances in a prokaryotic polysome. Mollweide projection histograms for each class highlighted in panel (a), depicts directions to each ribosome’s nearest neighbor ribosome, following rotation to the consensus pose.

(c) Distribution of k=20 k-means classification of latent embeddings per tomogram. Column width is proportional to each tomogram’s fraction of the total particle count. Within a column, the height of each color is proportional to the population of that k-means class within that tomogram. Classes are colored as in (a).

(d) Screenshot from tomoDRGN’s interactive tomogram viewer showing all ribosomes for a single tomogram (blue cones) with ribosomes corresponding to membrane-associated classes further annotated as red spheres.

(e) UMAP of tomoDRGN latent embeddings (n=482) of membrane-associated ribosomes. Colored volumes are sampled from correspondingly colored points in latent space. Relative occupancy of globular periplasmic density (n=482) is plotted as a histogram with a red line noting manually assigned threshold defining particles bearing the periplasmic density (n=380).

(f) STA reconstruction of membrane-associated ribosomes bearing periplasmic density identified by tomoDRGN with docked atomic model of Mycoplasma pneumoniae SecDF predicted using Alphafold (AF: A0A0H3DPH3).