Structural basis for the initiation of COPII vesicle biogenesis

The first stage of the eukaryotic secretory pathway is the packaging of cargo proteins into coat protein complex II (COPII) vesicles exiting the ER. The cytoplasmic COPII vesicle coat machinery is recruited to the ER membrane by the activated, GTP-bound, form of the conserved Sar1 GTPase. Activation of Sar1 on the surface of the ER by Sec12, a membrane-anchored GEF (guanine nucleotide exchange factor), is therefore the initiating step of the secretory pathway. Here we report the structure of the complex between Sar1 and the cytoplasmic GEF domain of Sec12, both from Saccharomyces cerevisiae. This structure, representing a key nucleotide-free activation intermediate, reveals how the potassium ion-binding K loop disrupts the nucleotide-binding site of Sar1. We propose an unexpected orientation of the GEF domain relative to the membrane surface and postulate a mechanism for how Sec12 facilitates membrane insertion of the amphipathic helix exposed by Sar1 upon GTP binding. [Display omitted] •We solved the structure of nucleotide-free Sar1 GTPase bound to its GEF, Sec12•The structure illuminates the mechanism of nucleotide exchange•An unexpected membrane-binding surface on Sec12 cytosolic domain is proposed•Sec12 may orient Sar1 for membrane insertion of its amphipathic helix The first step of the eukaryotic secretory pathway is formation of COPII vesicles at the endoplasmic reticulum. The COPII coat machinery is recruited by the Sar1 GTPase, which is activated via nucleotide exchange by Sec12. Joiner et al. determined the structure of the Sar1-Sec12 complex, representing a key activation intermediate.