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We hypothesize that protein clustering is important within synaptic vesicles, allowing the formation of pre-assembled functional units. Such units could efficiently preserve protein interactions critical for vesicle function, thereby facilitating the fast kinetics of the synaptic vesicle cycle. Although emerging evidence suggests that various proteins form clusters on the vesicle membrane, the lack of adequate tools has hindered the detailed study of these nano-compartments to date. We will address this here using cryo-electron tomography (cryo-ET).