Presenilin (PS) provides the catalytic core of the ␥-secretase complex. ␥-Secretase activity leads to generation of the amyloid -peptide, a key event implicated in the pathogenesis of Alzheimer disease. PS has ten hydrophobic regions, which can all theoretically form membrane-spanning domains. Various topology models have been proposed, and the prevalent view holds that PS has an eighttransmembrane (TM) domain organization; however, the precise topology has not been unequivocally determined. Previous topological studies are based on non-functional truncated variants of PS proteins fused to reporter domains, or immunocytochemical staining. In this study, we used a more subtle N-linked glycosylation scanning approach, which allowed us to assess the topology of functional PS1 molecules. Glycosylation acceptor sequences were introduced into full-length human PS1, and the results showed that the first hydrophilic loop is oriented toward the lumen of the endoplasmic reticulum, whereas the N terminus and large hydrophilic loop are in the cytosol. Although this is in accordance with most current models, our data unexpectedly revealed that the C terminus localized to the luminal side of the endoplasmic reticulum. Additional studies on the glycosylation pattern after TM domain deletions, combined with computer-based TM protein topology predictions and biotinylation assays of different PS1 mutants, led us to conclude that PS1 has nine TM domains and that the C terminus locates to the lumen/extracellular space.Most proteases operate in aqueous environments, but ␥-secretase, along with other intramembrane cleaving proteases, is unusual in the sense that it executes proteolysis in the lipid bilayer (1). ␥-Secretase is a high molecular weight protein complex composed of presenilin (PS) 2 1 or 2, nicastrin, Aph-1, and Pen-2 (2-5). Growing evidence suggests that the polytopic PS1 protein is a TM aspartyl protease and that two of its aspartate residues, Asp-257 in hydrophobic domain (HD) 6 and Asp-385 in HD 8, form the catalytic site of the ␥-secretase complex (6 -8). An endoproteolytic cleavage within HD 7 of PS1 generates an N-terminal fragment (NTF) and a C-terminal fragment (CTF) (9). The NTF/ CTF heterodimer is believed to be the biologically active form of PS. Nicastrin, Aph-1, and Pen-2 are all essential cofactors in the ␥-secretase complex, but their precise biochemical functions are not fully known. Nicastrin and Aph-1 have been proposed to form a subcomplex that can stabilize full-length PS, and the final addition of Pen-2 has been suggested to trigger PS endoproteolysis (10) and stabilize the NTF/CTF heterodimer (11). ␥-Secretase cleavage occurs within the lipid bilayer of the membrane through a mechanism referred to as "regulated intramembrane proteolysis" (12). Recently, not only APP, but a large number of other type-1 TM proteins, such as the Notch receptors, CD44 and E-cadherin, have been shown to undergo PS-dependent regulated intramembrane proteolysis (reviewed in Ref. 13). Given that target proteins of ␥-secret...