Luminal geometry and coiled coil length determine submembrane localization of type II transmembrane Golgi proteins

We previously showed that transmembrane proteins laterally partition within Golgi cisternae: trafficking components (e.g., GPP130, a type II transmembrane protein) are enriched at the cisternal rim, whereas Golgi enzymes localize to the cisternal interior. However, the underlying mechanism was unclear. We found that the luminal juxtamembrane coiled coil of GPP130 is necessary and sufficient for rim localization, with coiled coil length, rather than sequence identity, determining partitioning. When retargeted to the ER, GPP130 preferentially localized to ER sheet rims and was partially excluded from the nuclear envelope, an exclusion reduced upon nuclear envelope expansion. Cryo-electron tomography revealed that the intraluminal widths of Golgi cisternal interiors, some ER sheets, and the nuclear envelope are smaller than the predicted coiled coil length. Two additional type II Golgi transmembrane proteins with long luminal juxtamembrane coiled coils similarly localized to cisternal rims. These findings identify intraluminal width as a mechanism governing the lateral partitioning of type II transmembrane proteins with long luminal coiled coils. Wong et al. show that the intraluminal widths of the ER and Golgi and the length of luminal coiled coils of the transmembrane proteins determine localization, revealing a geometry-based localization mechanism.