Extended Data Fig. 11: V-ATPase as an interaction hub.
From: EndoMAP.v1 charts the structural landscape of human early endosome complexes
a, DSSO cross-links identified between components of the V-ATPase (purple), the BORC complex (red), the LAMTOR complex (blue) and RAB proteins (green). b, Hypothetical model for association of MTOR-Ragulator complex (PDB:7UXH)58 with V-ATPaseADP (PDB:6WM2)59 based on two DSSO cross-links between LAMTOR2 and LAMTOR4 with ATP6V1C1 (red lines). Docking model was generated using HADDOCK (see METHODS). c, Pairwise AF-M prediction and associated cross-link for MEAK7 and ATP6V1B2 (left) is compared with the MEAK7-ATP6V1B2 sub-complex from PDB:7U4T (right)171. d, MEAK7-V1-ATPase (PDB:7U4T)171 together with overlay of AF-M prediction for MEAK7-ATP6V1B2. Cross-links between MEAK7 and either ATP6V1B2 or ATP6V1D are shown by red lines172. e, MEAK7-ATP6V1B2 AF-M prediction modeled on PDB:7U4T and identified cross-links with ATP6V1D (red arrowhead) is shown on the left. MEAK7-ATP6V1D AF-M prediction and associated cross-link is shown on the right. f, Endosomal RABs cross-link with the ATPV0A1 subunit of the V0-ATPase. The structure of the V0-ATPase complex, with ATP6V0A1 shown in salmon, is presented on the far left. The AF-M predictions for 4 endosomal RABs and the detected cross-links are also shown. Intraprotein cross-links are not shown (see Supplementary Table 2). g, Screenshot from our EndoMAP.v1 website and AF-M prediction viewer at https://endomap.hms.harvard.edu/. Left panel shows the output of a search for TMEM230. Right panel shows the output of AF-M prediction for TMEM230-ATP11B interaction, together with predicted alignment error plots.
