Fig. 2: Assembly of an integrated endosome protein complex structural landscape.

a, Core component of the network containing 1,722 nodes organized into 41 communities (indicated by numbers) and 3,489 edges. Significantly enriched protein complexes of selected communities are provided in the top left (see Supplementary Table 2 for full list of communities). Diamonds and circular nodes represent high-confidence endosomal and other proteins, respectively. Solid and dashed edges represent interactions identified by at least one crosslink or only co-fractionating, respectively. Red edges indicate interaction previously reported. b, Distribution of path distances between proteins within and between the same complex compared with proteins without complex annotation. c, Distribution of fraction of direct neighbours in the same complex for each protein compared with a randomized network control. d, Systematic AF-M and AlphaLink2 predictions of protein interactions identified by XL–MS and match with the crosslink distance constraints. e, Distribution of Cα–Cα distances (Å) for interprotein DSSO crosslinks reflecting AF-M predictions with SPOC > 0.33 (orange) and SPOC < 0.33 (red). Only residues with pLDDT > 70 were considered. f, Distribution of AF-M ipTM scores and average pLDDT for predictions with ipTM > 0.3. Numbers of interprotein crosslinks evaluated and exceeding the DSSO crosslinker distance constraints are indicated by point size and the colour, respectively. g, Percentage of pairwise AF-M predictions with more or fewer than 50% of crosslinks within the distance constraint (orange and red, respectively) relative to the SPOC and ipTM score. h, ipTM scores for AF-M compared with AlphaLink2 predictions. Colour gradient represents the score difference; higher in AlphaLink2 (red) or AF-M (blue).

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