3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

Li, Xiaochun; Lu, Feiran; Trinh, Michael N.; Schmiege, Philip; Seemann, Joachim; Wang, Jiawei; Blobel, Günter

doi:10.1073/pnas.1711716114

3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

Journal Article · Mon Aug 07 00:00:00 EDT 2017 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1711716114· OSTI ID:1390867

Li, Xiaochun ^[1]; ^[2]; ^[2]; Schmiege, Philip ^[1]; Seemann, Joachim ^[2]; Wang, Jiawei ^[3]; Blobel, Günter ^[4]

Rockefeller Univ., New York, NY (United States); Univ. of Southwestern Medical Center, Dallas, TX (United States)
Univ. of Southwestern Medical Center, Dallas, TX (United States)
Tsinghua Univ., Beijing (China)
Rockefeller Univ., New York, NY (United States)

Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Here, all eight cysteines of the CTD form four disulfide bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: NIH

OSTI ID:: 1390867

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 34 Vol. 114; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (43)

Niemann-Pick Disease Type C: From Bench to Bedside Schiffmann, Raphael JAMA, Vol. 276, Issue 7 https://doi.org/10.1001/jama.1996.03540070057031	journal	August 1996
Structure of glycosylated NPC 1 luminal domain C reveals insights into NPC 2 and Ebola virus interactions Zhao, Yuguang; Ren, Jingshan; Harlos, Karl FEBS Letters, Vol. 590, Issue 5 https://doi.org/10.1002/1873-3468.12089	journal	February 2016
A coat of glycoconjugates on the inner surface of the lysosomal membrane in the rat kidney Neiss, W. F. Histochemistry, Vol. 80, Issue 6 https://doi.org/10.1007/BF02400979	journal	June 1984
Niemann-Pick disease type C Vanier, Marie Molecular and Chemical Neuropathology, Vol. 27, Issue 1 https://doi.org/10.1007/bf02815049	journal	January 1996
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen Zacarias, Sónia; Temporão, Adriana; Carpentier, Philippe JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 6 https://doi.org/10.1007/s00775-020-01814-y	journal	August 2020
Niemann-Pick Disease (Type C) Emery, Jared M.; Green, William R.; Huff, Dale S. American Journal of Ophthalmology, Vol. 74, Issue 6 https://doi.org/10.1016/0002-9394(72)90736-2	journal	December 1972
Role of lysosomal acid lipase in the metabolism of plasma low density lipoprotein. Observations in cultured fibroblasts from a patient with cholesteryl ester storage disease. Goldstein, Jl; Dana, Se; Faust, Jr Journal of Biological Chemistry, Vol. 250, Issue 21 https://doi.org/10.1016/S0021-9258(19)40786-2	journal	November 1975
Sterol Resistance in CHO Cells Traced to Point Mutation in SREBP Cleavage–Activating Protein Hua, Xianxin; Nohturfft, Axel; Goldstein, Joseph L. Cell, Vol. 87, Issue 3 https://doi.org/10.1016/S0092-8674(00)81362-8	journal	November 1996
The sterol-sensing domain: multiple families, a unique role? Kuwabara, Patricia E.; Labouesse, Michel Trends in Genetics, Vol. 18, Issue 4 https://doi.org/10.1016/S0168-9525(02)02640-9	journal	April 2002
The NPC1 protein: structure implies function Scott, Catherine; Ioannou, Y. A. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1685, Issue 1-3 https://doi.org/10.1016/j.bbalip.2004.08.006	journal	October 2004
Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol Kwon, Hyock Joo; Abi-Mosleh, Lina; Wang, Michael L. Cell, Vol. 137, Issue 7 https://doi.org/10.1016/j.cell.2009.03.049	journal	June 2009
Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection Gong, Xin; Qian, Hongwu; Zhou, Xinhui Cell, Vol. 165, Issue 6 https://doi.org/10.1016/j.cell.2016.05.022	journal	June 2016
Discovery of Oxysterol-Derived Pharmacological Chaperones for NPC1: Implication for the Existence of Second Sterol-Binding Site Ohgane, Kenji; Karaki, Fumika; Dodo, Kosuke Chemistry & Biology, Vol. 20, Issue 3 https://doi.org/10.1016/j.chembiol.2013.02.009	journal	March 2013
Identification of Surface Residues on Niemann-Pick C2 Essential for Hydrophobic Handoff of Cholesterol to NPC1 in Lysosomes Wang, Michael L.; Motamed, Massoud; Infante, Rodney E. Cell Metabolism, Vol. 12, Issue 2 https://doi.org/10.1016/j.cmet.2010.05.016	journal	August 2010
Simultaneous Targeting of NPC1 and VDAC1 by Itraconazole Leads to Synergistic Inhibition of mTOR Signaling and Angiogenesis Head, Sarah A.; Shi, Wei Q.; Yang, Eun Ju ACS Chemical Biology, Vol. 12, Issue 1 https://doi.org/10.1021/acschembio.6b00849	journal	December 2016
Ebola virus entry requires the host-programmed recognition of an intracellular receptor: Niemann-Pick C1 is a critical filovirus receptor Miller, Emily Happy; Obernosterer, Gregor; Raaben, Matthijs The EMBO Journal, Vol. 31, Issue 8 https://doi.org/10.1038/emboj.2012.53	journal	March 2012
Ebola virus entry requires the cholesterol transporter Niemann–Pick C1 Carette, Jan E.; Raaben, Matthijs; Wong, Anthony C. Nature, Vol. 477, Issue 7364 https://doi.org/10.1038/nature10348	journal	August 2011
Small molecule inhibitors reveal Niemann–Pick C1 is essential for Ebola virus infection Côté, Marceline; Misasi, John; Ren, Tao Nature, Vol. 477, Issue 7364 https://doi.org/10.1038/nature10380	journal	August 2011
Induction of asymmetrical cell division to analyze spindle-dependent organelle partitioning using correlative microscopy techniques Wei, Jen-Hsuan; Seemann, Joachim Nature Protocols, Vol. 4, Issue 11 https://doi.org/10.1038/nprot.2009.160	journal	October 2009
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Binding between the Niemann-Pick C1 protein and a photoactivatable cholesterol analog requires a functional sterol-sensing domain Ohgami, N.; Ko, D. C.; Thomas, M. Proceedings of the National Academy of Sciences, Vol. 101, Issue 34 https://doi.org/10.1073/pnas.0405255101	journal	August 2004
Niemann-Pick type C 1 function requires lumenal domain residues that mediate cholesterol-dependent NPC2 binding Deffieu, M. S.; Pfeffer, S. R. Proceedings of the National Academy of Sciences, Vol. 108, Issue 47 https://doi.org/10.1073/pnas.1110439108	journal	November 2011
Structure of human Niemann–Pick C1 protein Li, Xiaochun; Wang, Jiawei; Coutavas, Elias Proceedings of the National Academy of Sciences, Vol. 113, Issue 29 https://doi.org/10.1073/pnas.1607795113	journal	June 2016
Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2 Li, Xiaochun; Saha, Piyali; Li, Jian Proceedings of the National Academy of Sciences, Vol. 113, Issue 36 https://doi.org/10.1073/pnas.1611956113	journal	August 2016
Triazoles inhibit cholesterol export from lysosomes by binding to NPC1 Trinh, Michael N.; Lu, Feiran; Li, Xiaochun Proceedings of the National Academy of Sciences, Vol. 114, Issue 1 https://doi.org/10.1073/pnas.1619571114	journal	December 2016
Purified NPC1 Protein: I. BINDING OF CHOLESTEROL AND OXYSTEROLS TO A 1278-AMINO ACID MEMBRANE PROTEIN Infante, Rodney E.; Abi-Mosleh, Lina; Radhakrishnan, Arun Journal of Biological Chemistry, Vol. 283, Issue 2 https://doi.org/10.1074/jbc.M707943200	journal	November 2007
Purified NPC1 Protein: II. LOCALIZATION OF STEROL BINDING TO A 240-AMINO ACID SOLUBLE LUMINAL LOOP Infante, Rodney E.; Radhakrishnan, Arun; Abi-Mosleh, Lina Journal of Biological Chemistry, Vol. 283, Issue 2 https://doi.org/10.1074/jbc.M707944200	journal	November 2007
Niemann-Pick Type C1 I1061T Mutant Encodes a Functional Protein That Is Selected for Endoplasmic Reticulum-associated Degradation Due to Protein Misfolding Gelsthorpe, Mark E.; Baumann, Nikola; Millard, Elizabeth Journal of Biological Chemistry, Vol. 283, Issue 13 https://doi.org/10.1074/jbc.M708735200	journal	January 2008
Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann–Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis Rauniyar, Navin; Subramanian, Kanagaraj; Lavallée-Adam, Mathieu Molecular & Cellular Proteomics, Vol. 14, Issue 7 https://doi.org/10.1074/mcp.M114.045609	journal	April 2015
Mutations in NPC1 Highlight a Conserved NPC1-Specific Cysteine-Rich Domain Greer, Wl; Dobson, Mj; Girouard, Gs The American Journal of Human Genetics, Vol. 65, Issue 5 https://doi.org/10.1086/302620	journal	November 1999
Niemann-Pick C1 Disease: The I1061T Substitution Is a Frequent Mutant Allele in Patients of Western European Descent and Correlates with a Classic Juvenile Phenotype Millat, Gilles; Marçais, Christophe; Rafi, Mohammad A. The American Journal of Human Genetics, Vol. 65, Issue 5 https://doi.org/10.1086/302626	journal	November 1999
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Niemann-Pick C1 Disease Gene: Homology to Mediators of Cholesterol Homeostasis Carstea, E. D. Science, Vol. 277, Issue 5323 https://doi.org/10.1126/science.277.5323.228	journal	July 1997
Identification of HE1 as the Second Gene of Niemann-Pick C Disease Naureckiene, S. Science, Vol. 290, Issue 5500 https://doi.org/10.1126/science.290.5500.2298	journal	December 2000
A receptor-mediated pathway for cholesterol homeostasis Brown, Ms; Goldstein, Jl Science, Vol. 232, Issue 4746 https://doi.org/10.1126/science.3513311	journal	April 1986
Niemann-Pick disease type C Vanier, Marie T. Orphanet Journal of Rare Diseases, Vol. 5, Issue 1 https://doi.org/10.1186/1750-1172-5-16	journal	June 2010
Histone deacetylase inhibitors correct the cholesterol storage defect in most Niemann-Pick C1 mutant cells Pipalia, Nina H.; Subramanian, Kanagaraj; Mao, Shu Journal of Lipid Research, Vol. 58, Issue 4 https://doi.org/10.1194/jlr.M072140	journal	February 2017
Niemann-Pick Disease Type C Millichap, J. Gordon Pediatric Neurology Briefs, Vol. 3, Issue 9 https://doi.org/10.15844/pedneurbriefs-3-9-7	journal	September 1989
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Identification of NPC1 as the target of U18666A, an inhibitor of lysosomal cholesterol export and Ebola infection Lu, Feiran; Liang, Qiren; Abi-Mosleh, Lina eLife, Vol. 4 https://doi.org/10.7554/eLife.12177	journal	December 2015
Lysosomal membrane glycoproteins bind cholesterol and contribute to lysosomal cholesterol export Li, Jian; Pfeffer, Suzanne R. eLife, Vol. 5 https://doi.org/10.7554/eLife.21635	journal	September 2016

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Quantitating the epigenetic transformation contributing to cholesterol homeostasis using Gaussian process Wang, Chao; Scott, Samantha M.; Subramanian, Kanagaraj Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12969-x	journal	November 2019
Recent neuroimaging, neurophysiological, and neuropathological advances for the understanding of NPC Benussi, Alberto; Cotelli, Maria Sofia; Padovani, Alessandro F1000Research, Vol. 7 https://doi.org/10.12688/f1000research.12361.1	journal	January 2018
Simulations of NPC1(NTD):NPC2 Protein Complex Reveal Cholesterol Transfer Pathways Hodošček, Milan; Elghobashi-Meinhardt, Nadia International Journal of Molecular Sciences, Vol. 19, Issue 9 https://doi.org/10.3390/ijms19092623	journal	September 2018
NPC1 Deficiency in Mice is Associated with Fetal Growth Restriction, Neonatal Lethality and Abnormal Lung Pathology Rodriguez-Gil, Jorge L.; Watkins-Chow, Dawn E.; Baxter, Laura L. Journal of Clinical Medicine, Vol. 9, Issue 1 https://doi.org/10.3390/jcm9010012	journal	December 2019
Lysosomal cholesterol export reconstituted from fragments of Niemann-Pick C1 Trinh, Michael Nguyen; Brown, Michael S.; Seemann, Joachim eLife, Vol. 7 https://doi.org/10.7554/elife.38564	journal	July 2018
Niemann-Pick Disease Type C: Mutation Spectrum and Novel Sequence Variations in the Human NPC1 Gene Polese-Bonatto, Márcia; Bock, Hugo; Farias, Ana Carolina S. Molecular Neurobiology, Vol. 56, Issue 9 https://doi.org/10.1007/s12035-019-1528-z	journal	February 2019
Structural basis for itraconazole-mediated NPC1 inhibition Long, Tao; Qi, Xiaofeng; Hassan, Abdirahman Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-13917-5	journal	January 2020
Structures of human Patched and its complex with native palmitoylated sonic hedgehog Qi, Xiaofeng; Schmiege, Philip; Coutavas, Elias Nature, Vol. 560, Issue 7716 https://doi.org/10.1038/s41586-018-0308-7	journal	July 2018
Different Niemann-Pick C1 Genotypes Generate Protein Phenotypes that Vary in their Intracellular Processing, Trafficking and Localization Shammas, Hadeel; Kuech, Eva-Maria; Rizk, Sandra Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41707-y	journal	March 2019
Rapid, direct activity assays for Smoothened reveal Hedgehog pathway regulation by membrane cholesterol and extracellular sodium Myers, Benjamin R.; Neahring, Lila; Zhang, Yunxiao Proceedings of the National Academy of Sciences, Vol. 114, Issue 52 https://doi.org/10.1073/pnas.1717891115	journal	December 2017
NPC intracellular cholesterol transporter 1 (NPC1)-mediated cholesterol export from lysosomes Pfeffer, Suzanne R. Journal of Biological Chemistry, Vol. 294, Issue 5 https://doi.org/10.1074/jbc.tm118.004165	journal	February 2019
Modeling Niemann–Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation Erwood, Steven; Brewer, Reid A.; Bily, Teija M. I. Genome Research, Vol. 29, Issue 12 https://doi.org/10.1101/gr.250720.119	journal	November 2019
AcrB: a mean, keen, drug efflux machine Kobylka, Jessica; Kuth, Miriam S.; Müller, Reinke T. Annals of the New York Academy of Sciences, Vol. 1459, Issue 1 https://doi.org/10.1111/nyas.14239	journal	September 2019
Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain Dubey, Vikas; Bozorg, Behruz; Wüstner, Daniel PLOS Computational Biology, Vol. 16, Issue 10 https://doi.org/10.1371/journal.pcbi.1007554	journal	October 2020
Lipid–Protein Interactions in Niemann–Pick Type C Disease: Insights from Molecular Modeling Wheeler, Simon; Schmid, Ralf; Sillence, Dan J. International Journal of Molecular Sciences, Vol. 20, Issue 3 https://doi.org/10.3390/ijms20030717	journal	February 2019

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59 BASIC BIOLOGICAL SCIENCES
Niemann–Pick type C disease
cholesterol transport
crystal structure
cysteine-rich domain
sterol-sensing domain

3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

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