Single-molecule FRET-derived model of the synaptotagmin 1–SNARE fusion complex

Synchronous neurotransmission is triggered when Ca(2+) binds to synaptotagmin 1, a synaptic vesicle protein that interacts with SNAREs and membranes. We used single-molecule FRET between synaptotagmin’s two C2 domains to determine that their conformation consists of multiple states with occasional transitions, consistent with domains in random relative motion. SNARE binding results in narrower intra-synaptotagmin FRET distributions and less frequent transitions between states. We obtained an experimentally determined model of the elusive synaptotagmin 1–SNARE complex by using a multi-body docking approach with 34 FRET-derived distances as restraints. The Ca(2+)-binding loops point away from the SNARE complex, so they could interact with the same membrane. The loop arrangement is similar to that of the crystal structure of SNARE-induced Ca(2+) bound synaptotagmin 3, suggesting a common mechanism by which the interaction between synaptotagmins and SNAREs plays a role in Ca(2+)-triggered fusion.