Edited by George M. CarmanScap is a polytopic protein of endoplasmic reticulum (ER) membranes that transports sterol regulatory element-binding proteins to the Golgi complex for proteolytic activation. Cholesterol accumulation in ER membranes prevents Scap transport and decreases cholesterol synthesis. Previously, we provided evidence that cholesterol inhibition is initiated when cholesterol binds to loop 1 of Scap, which projects into the ER lumen. Within cells, this binding causes loop 1 to dissociate from loop 7, another luminal Scap loop. However, we have been unable to demonstrate this dissociation when we added cholesterol to isolated complexes of loops 1 and 7. We therefore speculated that the dissociation requires a conformational change in the intervening polytopic sequence separating loops 1 and 7. Here we demonstrate such a change using a protease protection assay in sealed membrane vesicles. In the absence of cholesterol, trypsin or proteinase K cleaved cytosolic loop 4, generating a protected fragment that we visualized with a monoclonal antibody against loop 1. When cholesterol was added to these membranes, cleavage in loop 4 was abolished. Because loop 4 is part of the so-called sterol-sensing domain separating loops 1 and 7, these results support the hypothesis that cholesterol binding to loop 1 alters the conformation of the sterol-sensing domain. They also suggest that this conformational change helps transmit the cholesterol signal from loop 1 to loop 7, thereby allowing separation of the loops and facilitating the feedback inhibition of cholesterol synthesis. These insights suggest a new structural model for cholesterol-mediated regulation of Scap activity.A membrane protein called Scap controls cholesterol homeostasis in animal cells. Scap facilitates the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), 6 transcription factors that activate the genes encoding all of the enzymes required for synthesis of cholesterol and unsaturated fatty acids and their uptake from circulating plasma LDL (2). Scap is also the cholesterol sensor that turns off SREBP processing when cellular cholesterol levels are too high. Our laboratory has made recent progress in understanding the mechanism for this cholesterol regulation through a delineation of the conformational changes cholesterol produces when it binds to Scap (1, 3).Scap is a polytopic membrane protein with eight transmembrane helices that is synthesized on endoplasmic reticulum (ER) membranes (4). The carboxyl-terminal domain of Scap projects into the cytosol, where it binds to the cytosolic regulatory domain of SREBPs (5). Like Scap, SREBPs are synthesized on ER-bound ribosomes. Immediately after their synthesis, SREBPs bind to Scap. When ER cholesterol levels are low, Scap serves as the binding site for coat protein complex II (COPII) proteins that incorporate the Scap/SREBP complex into COPIIcoated vesicles that move to the Golgi (6). There the SREBPs are processed proteolytically to release their active transcription ...