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Clathrin-coated vesicles (CCVs) play critical roles in multiple cellular processes, including nutrient uptake, endosome/lysosome biogenesis, pathogen invasion, regulation of signalling receptors, etc. Saccharomyces cerevisiae Ent5 ( Sc Ent5) is one of the two major adaptors supporting the CCV-mediated TGN/endosome traffic in yeast cells. However, the classification and phosphoinositide binding characteristic of Sc Ent5 remain elusive. Here we report the crystal structures of the Sc Ent5 N-terminal domain, and find that Sc Ent5 contains an insertion α′ helix that does not exist in other ENTH or ANTH domains. Furthermore, we investigate the classification of Sc Ent5-N 31−191 by evolutionary history analyses and structure comparisons, and find that the Sc Ent5 N-terminal domain shows different phosphoinositide binding property from r Epsin1 and r CALM. Above results facilitate the understanding of the Sc Ent5-mediated vesicle coat formation process. [ABSTRACT FROM AUTHOR]