This deposit contains alphafold predictions (.pdb and .json files) for alphafold multimer predictions of protein pairs and 3-way cliques identified by cross linking proteomics with DSSO crosslinker in the context of purified EEA1-positive endosomes. Predictions were made with alphafold multimer (ColabFold v 1.5.2 )[Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat Methods 19, 679-682 (2022). https://doi.org:10.1038/s41592-022-01488-1]. Reference: Gonzalez-Lozano, M.A., Schmid, E.W., Miguel Whelan, E. et al. EndoMAP.v1 charts the structural landscape of human early endosome complexes. Nature 643, 252–261 (2025). https://doi.org/10.1038/s41586-025-09059-y