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The intracellular localization of ABCB6 has been a matter of debate, as it has been suggested to reside in the mitochondria and the endo-lysosomal system. Using a variety of imaging modalities including confocal and electron microscopy we confirm the endo-lysosomal localization of ABCB6 and show that the protein is internalized from the plasma membrane through endocytosis, to be distributed to multivesicular bodies and lysosomes. In addition to the canonical nucleotide binding (NBD) and transmembrane domains (TMD), ABCB6 contains a unique N-terminal transmembrane domain (TMD0), which does not show sequence homology to known proteins. We investigated the functional role of these domains through the molecular dissection of ABCB6. We find that the folding, dimerization, membrane insertion and ATP binding/hydrolysis of the core ABCB6 complex devoid of TMD0 is preserved. However, in contrast to the full-length transporter, the core ABCB6 construct is retained at the plasma membrane, and does not appear in Rab5-positive endosomes. TMD0 is directly targeted to the lysosomes, without a passage to the plasma membrane. 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