The SNARE proteins VAMP/synaptobrevin, SNAP-25 and Syntaxin are core components of the apparatus that mediates neurotransmitter release. They form a heterotrimeric complex and an undetermined number of SNARE complexes assemble to form a super-complex. Here, we present a radial model of this nanomachine, derived from experiments performed with botulinum neurotoxins, which led to the identification of one arginine in SNAP-25 and one aspartate in Syntaxin (R206 and D253 in Drosophila melanogaster). These residues are highly conserved and predicted to play a major role in the protein-protein interactions among SNARE complexes by forming an ionic couple. Accordingly, we generated transgenic Drosophila lines expressing SNAREs mutated in these residues and performed an electrophysiological analysis of their neuromuscular junctions. Our results indicate that SNAP-25-R206 and Syntaxin-D253 play a major role in neuroexocytosis and support a radial assembly of several SNARE complexes interacting via the ionic couple formed by these two residues.