Fig. 2: Maps of V-ATPases imaged in wild-type and Syp−/− ISVs.
From: Structure and topography of the synaptic V-ATPase–synaptophysin complex
a,b, SPA maps of intact (a; state 3) and V0-only (b) V-ATPase assemblies imaged in wild-type (WT) ISVs. The V-ATPase subunits are coloured as indicated, and the extra binding partner density is coloured in orange. The background grey arc represents the ISV membrane density. Scale bars, 5 nm. c, Docking of models into the binding partner density (orange) extracted from the map shown in a. The solution NMR structure of synaptogyrin-1 and the AlphaFold2 predicted atomic models of synaptogyrin-3, synaptoporin and synaptophysin are shown. The atomic models are shown in cartoon representation and coloured in yellow and blue to indicate if the model is in the interior or the exterior of the map, respectively. For clarity, only the transmembrane and luminal parts are displayed, omitting the cytosolic regions that are predicted to be unstructured. Scale bar, 5 nm. d, Representative western blots (one of nine independent measurements) of synaptic proteins in LP2 and ISV samples from wild-type and Syp−/− ISVs (Extended Data Fig. 4). Abs, antibodies. e, Dynamic light scattering (DLS) measurements of wild-type and Syp−/− ISVs. The means and standard deviations of the ISV diameters were calculated from three independent ISV preparations. P-values were calculated by the unpaired two-tailed t-test. NS, not significant. f, Size distribution analysis of wild-type and Syp−/− ISVs by inspection of cryo-EM images. The mean ± s.d. of wild-type and Syp−/− ISV diameters were calculated from 326 wild-type ISVs and 362 Syp−/− ISVs, respectively. In the violin plots, the bottom dotted line represents the first quartile, the middle dashed line represents the median, and the top dotted line represents the third quartile. P-values were calculated by unpaired two-tailed t-test. g,h, SPA maps of intact (g; state 3) and V0-only (h) V-ATPase assemblies imaged in Syp−/− ISVs. The V-ATPase subunits are coloured as in a and b. The corresponding location of the binding partner density identified in wild-type ISVs is indicated as a dashed orange silhouette for comparison. The background grey arc represents the ISV membrane density. Scale bars, 5 nm.
