BORC assemblies integrate BLOC-1 subunits to diversify endosomal trafficking functions

BORC and BLOC-1, evolutionarily conserved since the last eukaryotic common ancestor, orchestrate endocytic trafficking. We show that the 3D architecture of BORC - two tetramers of intertwined α-helices with N-termini converging at the core - is conserved across species. Integrative structural approaches identified assembly-critical residues and elucidated disease mutation mechanisms. Strikingly, BORC and BLOC-1 components integrate into common complexes, with BORC-disrupting mutations also impairing BLOC-1 specific components incorporation. Crosslinking mass spectrometry analysis confirmed the in vivo presence of one BORC/BLOC-1 module. EARP subunits interact with BORC/BLOC-1 mixed complexes, suggesting that a subset of the hybrid assemblies regulates recycling. These findings challenge the view of BORC and BLOC-1 as distinct entities and instead support context-dependent assembly. We propose that dynamic, modular configurations enable specialized trafficking roles.