Structure of human Niemann–Pick C1 protein

Significance Niemann–Pick C1 protein (NPC1) is a late-endosomal membrane protein required for transport of LDL-derived cholesterol into cells and Ebola virus entry; mutations cause Niemann–Pick type C disease. NPC1 contains a “sterol-sensing domain” (SSD) that also appears in several key regulatory proteins of cholesterol biosynthesis, uptake, and signaling. We present here the crystal structure of a large portion of human NPC1, which reveals the architecture of the SSD, including a cavity that is accessible both vertically to the endosome lumen and laterally to the “luminal” leaflet of the lipid bilayer. We propose that NPC1’s SSD functions in a pocket-relay system for cholesterol transport, the activity of which is regulated by the cholesterol concentration of the adjacent lipid bilayer. Niemann–Pick C1 protein (NPC1) is a late-endosomal membrane protein involved in trafficking of LDL-derived cholesterol, Niemann–Pick disease type C, and Ebola virus infection. NPC1 contains 13 transmembrane segments (TMs), five of which are thought to represent a “sterol-sensing domain” (SSD). Although present also in other key regulatory proteins of cholesterol biosynthesis, uptake, and signaling, the structure and mechanism of action of the SSD are unknown. Here we report a crystal structure of a large fragment of human NPC1 at 3.6 Å resolution, which reveals internal twofold pseudosymmetry along TM 2–13 and two structurally homologous domains that protrude 60 Å into the endosomal lumen. Strikingly, NPC1's SSD forms a cavity that is accessible from both the luminal bilayer leaflet and the endosomal lumen; computational modeling suggests that this cavity is large enough to accommodate one cholesterol molecule. We propose a model for NPC1 function in cholesterol sensing and transport.

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