Sec1/Munc18 proteins (SM proteins) bind to soluble NSF attachment protein receptors (SNAREs) and play an essential role in membrane fusion. Divergent modes of regulation have been proposed for different SM proteins indicating that they can either promote or inhibit SNARE assembly. This is in part because of discrete modes of binding that have been described for various SM/SNARE complexes. One mode suggests that SM proteins bind only to Syntaxins (Stx) preventing SNARE assembly, whereas in another they facilitate SNARE assembly and bind to SNARE complexes. The mammalian cell surface SM protein Munc18c binds to an N-peptide in Stx4, and this is compatible with its interaction with SNARE complexes. Here we describe the crystal structure of Munc18c in complex with the Stx4 N-peptide. This structure shows remarkable similarity with a yeast complex indicating that the mode of binding, which can accommodate SNARE complexes, is highly conserved throughout evolution. Modeling reveals the presence of the N-peptide binding mode in most but not all yeast and mammalian SM/Stx pairs, suggesting that it has coevolved to fulfill a specific regulatory function. It is unlikely that the N-peptide interaction alone accounts for the specificity in SM/SNARE binding, implicating other contact surfaces in this function. Together with other data, our results support a sequential two-state model for SM/SNARE binding involving an initial interaction via the Stx N-peptide, which somehow facilitates a second, more comprehensive interaction comprising other contact surfaces in both proteins. crystallography ͉ protein:protein interactions ͉ vesicle trafficking I ntracellular trafficking relies on membrane fusion, a tightly regulated process that requires the formation of a coiled coil complex between helical motifs originating from soluble NSF attachment protein receptor (SNARE) proteins on vesicle and target membranes (1-3). Sec1/Munc18 proteins (SM proteins) play a fundamental role in this process by interacting with SNARE protein(s) and regulating the formation of SNARE complexes (4, 5). SM proteins have been identified in organisms from yeast to humans, and loss-of-function mutants lead to severe impairment in vesicle fusion (6).Despite their obvious importance, the nature of SNARE regulation by SM proteins remains controversial, in that both positive and negative regulatory roles have been reported (6, 7). Possibly the most compelling evidence in support of negative regulation is the observation that the mammalian Syntaxin1a (Stx1a) SNARE protein involved in synaptic neurotransmission exists in both an ''open'' (SNARE complex-compatible) and a ''closed'' (SNARE complexincompatible) conformation (8, 9). The crystal structure of Stx1a in complex with the SM protein Munc18-1 (Munc18a, nSec1) reveals that Munc18-1 embraces a closed conformation preventing Stx1a from forming the SNARE complex required for vesicle fusion (10). On the other hand, deletion of Munc18-1 results in impaired exocytosis in mouse neurons and chromaffin cells (11, 12),...