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SUMMARY While misfolding of alpha-synuclein (αSyn) is central to the pathogenesis of Parkinson’s disease (PD), fundamental questions about its structure and function at the synapse remain unanswered. We examine synaptosomes from non-transgenic and transgenic mice expressing wild-type human αSyn, the E46K fPD-causing mutation, or an amplified form of E46K (“3K”). Synaptosomes from mice expressing the 3K mutant show reduced Ca2+-dependent vesicle exocytosis, altered synaptic vesicle ultrastructure, decreased SNARE complexes, and abnormal levels of certain synaptic proteins. With our intra-synaptosomal nuclear magnetic resonance (NMR) method, we reveal that WT αSyn participates in heterogeneous interactions with synaptic components dependent on endogenous αSyn and synaptosomal integrity. The 3K mutation markedly alters these interactions. The synaptic microenvironment is necessary for αSyn to reach its native conformations and establish a physiological interaction network. Its inability to populate diverse conformational ensembles likely represents an early step in αSyn dysfunction that contributes to the synaptotoxicity observed in synucleinopathies., In brief Fonseca-Ornelas et al. report the in-cell NMR behavior of αSyn at synapses. While WT αSyn participates in transient interactions with synaptic components, an αSyn variant based on an fPD mutant displays a reduced ability to do so. This results in biochemical, morphological, and functional changes that may explain αSyn-related toxicity., Graphical Abstract