SNARE proteins are crucial for membrane fusion in vesicular transport. To ensure efficient and accurate fusion, SNAREs need to be sorted into different budding vesicles. This process is usually regulated by specific recognition between SNAREs and their adaptor proteins. How different pairs of SNAREs and adaptors achieve their recognition is unclear. Here, we report the recognition between yeast SNARE Vti1p and its adaptor Ent3p derived from three crystal structures. Surprisingly, this yeast pair Vti1p/Ent3p interacts through a distinct binding site compared to their homologues vti1b/epsinR in mammals. An opposite surface on Vti1p_Habc domain binds to a conserved area on the epsin N-terminal homology (ENTH) domain of Ent3p. Two-hybrid, in vitro pull-down and in vivo experiments indicate this binding interface is important for correct localization of Vti1p in the cell. This previously undescribed discovery that a cargo and adaptor pair uses different binding sites across species suggests the diversity of SNARE-adaptor recognition in vesicular transport.cargo recogniton | Vti1p sorting | crystallography S ecretion and intracellular transport rely on vesicular traffic in eukaryotic cells. Vesicle transport can be divided into multiple steps: budding, targeting, tethering, and fusion (1). During the fusion process, the vesicles fuse with the target membrane and release the cargo proteins. The key players in membrane fusion are SNAREs (soluble N-ethylmaleimide-sensitive factor attachment receptor) (2, 3). SNARE proteins are defined by their characteristic heptad repeat SNARE domains. During the fusion process, four SNARE domains (usually one on the vesicle membrane and three on the target membrane) associate to form a stable twisted four-helix bundle, bringing the two opposing membranes in close contact and facilitating fusion (3). Thus, SNAREs are regarded as the basic element in membrane fusion (2-4).Vesicle fusions are specific processes that require the specific localization of SNAREs on different membranes. There are 24 SNAREs in yeast and about 40 SNAREs in mammals with specific subcellular localization (5-7) (Fig. S1). SNAREs are recruited as cargo proteins to different subcellular membranes by adaptor proteins (8). The maintenance of compartment identity requires highly specific recognition between SNAREs and their adaptor proteins during vesicle budding. Distinct from many cargo proteins, most SNAREs do not contain the short, linear sorting motifs that are recognized by common adaptors like AP or GGA for sorting into vesicles (there are few exceptions including Vamp4, which contains the signal motif dileucine recognized by AP) (9-11). It has been reported, however, that the N-terminal three-helix bundle (Habc domain) of many SNAREs is recognized through interaction with the ENTH (epsin N-terminal homology) domain of a few epsin-like family proteins (8,12,13).The epsin-like family is characterized by a conserved N-terminal ENTH domain (11,14,15) and consists of four epsin proteins (epsin1, epsin2, epsin3, epsi...