Structural Basis of the Intracellular Sorting of the SNARE VAMP7 by the AP3 Adaptor Complex

Summary VAMP7 is involved in the fusion of late endocytic compartments with other membranes. One possible mechanism of VAMP7 delivery to these late compartments is via the AP3 trafficking adaptor. We show that the linker of the δ-adaptin subunit of AP3 binds the VAMP7 longin domain and determines the structure of their complex. Mutation of residues on both partners abolishes the interaction in vitro and in vivo. The binding of VAMP7 to δ-adaptin requires the VAMP7 SNARE motif to be engaged in SNARE complex formation and hence AP3 must transport VAMP7 when VAMP7 is part of a cis-SNARE complex. The absence of δ-adaptin causes destabilization of the AP3 complex in mouse mocha fibroblasts and mislocalization of VAMP7. The mislocalization can be rescued by transfection with wild-type δ-adaptin but not by δ-adaptin containing mutations that abolish VAMP7 binding, despite in all cases intact AP3 being present and LAMP1 trafficking being rescued.
Graphical Abstract Highlights ► AP3-containing vesicles transport VAMP7 and LAMP1 from early to late endosomes ► The ear/trunk linker of the AP3 δ-subunit binds in a groove on a VAMP7 longin domain ► Binding of VAMP by AP3 can only occur when VAMP is part of a cis-SNARE complex ► VAMP7 is not required for the fusion of AP3-containing vesicles with late endosomes
VAMP7 SNARE complexes on late endosomes determine the specificity of membrane fusion there. But how is VAMP7 localization maintained? Kent et al. define the structure of and requirement for VAMP7 interactions with the cargo adaptor AP3. AP3 uses distinct surfaces for VAMP7 versus other cargoes to recycle postfusion cis-SNARE complexes.