Structural Basis of Low-pH-Dependent Lysosomal Cholesterol Egress by NPC1 and NPC2

• Published in: Cell Vol. 182; no. 1; pp. 98 - 111.e18
• Main Authors: Qian, Hongwu, Wu, Xuelan, Du, Ximing, Yao, Xia, Zhao, Xin, Lee, Joyce, Yang, Hongyuan, Yan, Nieng
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09.07.2020
• Subjects: Amino Acid Sequence; Animals; Cell Line; cholesterol; Cholesterol - metabolism; cholesterol transport; cryo-EM; detergents; Green Fluorescent Proteins - metabolism; Humans; Hydrogen-Ion Concentration; Intracellular Signaling Peptides and Proteins - chemistry; Intracellular Signaling Peptides and Proteins - metabolism; lysosomal cholesterol egress; Lysosomes - metabolism; Models, Molecular; Nanoparticles - chemistry; Nanoparticles - ultrastructure; Niemann-Pick disease type C; NPC1; NPC2; Protein Domains; proteins; structural biology; Structural Homology, Protein; Structure-Activity Relationship; Vesicular Transport Proteins - chemistry; Vesicular Transport Proteins - metabolism; cholesterol transport; NPC1; NPC2; lysosomal cholesterol egress; structural biology; Niemann-Pick disease type C; cryo-EM
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2020.05.020

Lysosomal cholesterol egress requires two proteins, NPC1 and NPC2, whose defects are responsible for Niemann-Pick disease type C (NPC). Here, we present systematic structural characterizations that reveal the molecular basis for low-pH-dependent cholesterol delivery from NPC2 to the transmembrane (TM) domain of NPC1. At pH 8.0, similar structures of NPC1 were obtained in nanodiscs and in detergent at resolutions of 3.6 Å and 3.0 Å, respectively. A tunnel connecting the N-terminal domain (NTD) and the transmembrane sterol-sensing domain (SSD) was unveiled. At pH 5.5, the NTD exhibits two conformations, suggesting the motion for cholesterol delivery to the tunnel. A putative cholesterol molecule is found at the membrane boundary of the tunnel, and TM2 moves toward formation of a surface pocket on the SSD. Finally, the structure of the NPC1-NPC2 complex at 4.0 Å resolution was obtained at pH 5.5, elucidating the molecular basis for cholesterol handoff from NPC2 to NPC1(NTD). [Display omitted] •Cryo-EM structure of NPC1 embedded in nanodiscs was determined at 3.6 Å resolution•Distinct conformations of NPC1-SSD at pH 5.5 and 8.0 suggest pH dependency•Two states of NPC1-NTD and a sterol-bearing central tunnel were resolved at pH 5.5•The cryo-EM structure of full-length NPC2/ NPC1 complex was determined at 4.0 Å Structural analyses of NPC1 and its complex with NPC2 reveal the basis for low-pH-dependent cholesterol delivery from the lysosomal lumen to the membrane and provide insights into the effects of more than 200 mutations associated with Niemann-Pick disease type C.