SNARE proteins are required for intracellular membrane fusion. In the neuron, the plasma membrane SNAREs syntaxin 1a and SNAP25 bind to VAMP2 found on neurotransmitter-containing vesicles. These three proteins contain "SNARE regions" that mediate their association into stable tetrameric coiled-coil structures. Syntaxin 1a contributes one such region, designated H3, and SNAP25 contributes two SNARE regions to the fusogenic complex with VAMP2. Syntaxin 1a H3 (syn1aH3) and SNAP25 can form a stable assembly, which can then be bound by VAMP2 to form the full SNARE complex. Here we show that syn1aH3 can also form a stable but kinetically trapped complex with the N-terminal SNARE region of SNAP25 (S25N). The crystal structure of this complex reveals an extended parallel four-helix bundle similar to that of the core SNARE and the syn1aH3⅐SNAP25 complexes. The inherent ability of syn1aH3 and S25N to associate stably in vitro implies that the intracellular fusion machinery must prevent formation of, or remove, any nonproductive complexes. Comparison with the syn1aH3⅐SNAP25 complex suggests that the linkage of the N-and C-terminal SNAP25 SNARE regions is kinetically advantageous in preventing formation of the non-productive syn1aH3⅐S25N complex. We also demonstrate that the syn1aH3⅐S25N complex can be disassembled by ␣-SNAP and N-ethylmaleimide-sensitive factor.Eukaryotic cells maintain highly organized membrane structures to perform essential cellular functions such as protein synthesis, modification, and degradation. Communication between these membrane compartments is essential to ensure that proteins and other molecules are transported and segregated into appropriate organelles within the cell. This is achieved through cargo-containing vesicles that bud from donor membranes and are transported to acceptor membranes where they fuse. Such a process allows local rearrangement of lipid bilayers while maintaining the overall structural integrity of the membrane compartment. Membrane fusion is mediated in part by a large family of compartment-specific proteins known as SNAREs 1 (soluble NSF attachment protein receptors) that are localized on vesicle or target membranes (1, 2).In neurons, the SNAREs syntaxin 1a (syn1a), SNAP25, and VAMP2 participate in fusing neurotransmitter-filled vesicles with the plasma membrane of the cell, allowing neurotransmitter molecules to be released into the synaptic cleft. VAMP2 (also known as synaptobrevin) is found on the vesicle membrane and contains a characteristic "SNARE region" heptad repeat sequence followed by a single C-terminal membranespanning segment (3). Syntaxin 1a and SNAP25 are localized to the presynaptic membrane. The primary structure of syntaxin 1a consists of an N-terminal domain termed Habc, a SNARE region termed H3, and a single C-terminal membranespanning anchor (4, 5). SNAP25 contains two SNARE regions, designated S25N and S25C, that are separated by a linker region containing four palmitoylated cysteines that tether the protein to the membrane (6, 7). The four SNARE re...