Structural basis for LMBD1-dependent trafficking and cobalamin export of ABCD4

Correct trafficking of lysosomal transporters is essential for intracellular homeostasis. While most lysosomal membrane proteins are directed to the lysosome via sorting motifs, the cobalamin exporter ABCD4 is distinct, instead relying on LMBD1 as a dedicated chaperone for its trafficking. Dysfunction of either protein causes inherited cobalamin metabolism disorders. Despite its physiological significance, the molecular mechanism underlying this chaperone-dependent trafficking remains unclear. Here, we report the cryo-EM structures of ABCD4 complex with LMBD1 in the lumen-open, substrate-bound and cytosol-open states. LMBD1 contains nine transmembrane-helices (TMs) and a cytosolic domain, both of which engage ABCD4. Cell imaging shows that disruption of these interactions impairs the trafficking of ABCD4 to lysosomes. Structural and biochemical analyses provide insights into cobalamin recognition and reveal conformational states associated with the proposed cobalamin transport cycle. These findings provide molecular insights into cobalamin metabolism and illustrate a chaperone-assisted mechanism that supports proper trafficking of a lysosomal transporter. Proper localization of lysosomal transporters supports cellular homeostasis. Here, the authors present cryo-EM structures of the ABCD4–LMBD1 complex in multiple conformational states, providing insights into cobalamin metabolism and the trafficking of a lysosomal transporter.