Extended Data Fig. 10: Endosomal Regulatory Proteins, Channels, Cargo, and Trafficking Complex AF-M Predictions.
From: EndoMAP.v1 charts the structural landscape of human early endosome complexes
a, Pairwise AF-M predictions and associated cross-links for two pairs of RABs with high scoring predictions. b,c, Pairwise AF-M predictions and associated cross-links for selected RABGEF complexes present in EndoMAP.v1 (panel b), and for a RAB11A-SH3BP5 complex (panel c) overlayed with a previously determined structure of the complex (PDB:6DJL). d, Pairwise AF-M prediction and associated cross-links for a RAB8A-SYTL4 (synaptotagmin-like) Snare complex. e-g, AF-M predictions and associated cross-links for selected channel/transporter assemblies in EndoMAP.v1. LRRC8 proteins (panel e) form hexamers and are components of volume regulated anion channels important for cell volume homeostasis. OSTM1-CLCN7 (panel f) is an endolysosomal voltage-gated channel mediating exchange of chloride against protons and is known to form a heterotetramer. CLCN7 was found cross-linked to RMC1 (panel g), a subunit of the CCZ1-MON1 GEF for RAB7 on endolysosomes. h, Pairwise AF-M predictions for cross-link containing AP1 components AP1G1 and either AP1S1 or AP1S2 (left) and tetramer AF-M prediction for AP1G1-AP1B1-AP1M1 and either AP1S1 or AP1S2 (upper panel). Pairwise and 3-way clique predictions for AP2 components AP2M1, AP2B1, or AP2A2 (lower panel). i, Pairwise predictions and associated cross-links for ESCRT and ubiquitin (Ub)-related modules within EndoMAP.v1. j, Pairwise predictions and associated cross-links for INSR and IGF1R. k, Pairwise AF-M predictions and associated cross-links for selected HOPS complex components (left) and a 3-way clique prediction (right) that maintains compatible cross-link distances. l, Pairwise predictions and associated cross-links for the FLOT1/2 complex that participates as a scaffolding protein within caveolar membranes, and the ITSN1-EPS15L complex that links endosomal membrane trafficking with actin assembly machinery. For all panels, DSSO and DHSO/DMTMM interprotein cross-links are indicated with red and cyan lines and arrowheads, respectively. Intraprotein cross-links are not shown (see Supplementary Table 2).
