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Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition

Journal Article · · Science Advances
 [1];  [1];  [2];  [1];  [1];  [3];  [4];  [2];  [1];  [1]
  1. Amgen Inc., South San Francisco, CA (United States). Dept. of Therapeutic Discovery
  2. Amgen Inc., South San Francisco, CA (United States). Dept. of Cardiometabolic Disorders
  3. Stanford Univ., CA (United States). Dept. of Bioengineering and James H. Clark Center
  4. Stanford Univ., CA (United States). Dept. of Bioengineering and James H. Clark Center; SLAC National Accelerator Lab., Menlo Park, CA (United States). Division of Cryo-EM and Bioimaging
The intestinal absorption of cholesterol is mediated by a multipass membrane protein, Niemann-Pick C1-Like 1 (NPC1L1), the molecular target of a cholesterol lowering therapy ezetimibe. While ezetimibe gained Food and Drug Administration approval in 2002, its mechanism of action has remained unclear. Here, we present two cryo–electron microscopy structures of NPC1L1, one in its apo form and the other complexed with ezetimibe. The apo form represents an open state in which the N-terminal domain (NTD) interacts loosely with the rest of NPC1L1, leaving the NTD central cavity accessible for cholesterol loading. The ezetimibe-bound form signifies a closed state in which the NTD rotates ~60°, creating a continuous tunnel enabling cholesterol movement into the plasma membrane. Ezetimibe blocks cholesterol transport by occluding the tunnel instead of competing with cholesterol binding. These findings provide insight into the molecular mechanisms of NPC1L1-mediated cholesterol transport and ezetimibe inhibition, paving the way for more effective therapeutic development.
Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
National Institutes of Health (NIH); National Research Foundation of Korea (NRF); USDOE Office of Science (SC)
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1647629
Journal Information:
Science Advances, Journal Name: Science Advances Journal Issue: 25 Vol. 6; ISSN 2375-2548
Publisher:
AAASCopyright Statement
Country of Publication:
United States
Language:
English

References (59)

UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Evidence for a Niemann–Pick C (NPC) Gene Family: Identification and Characterization of NPC1L1 journal April 2000
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht journal February 1999
Pharmacological Options in Atherosclerosis: A Review of the Existing Evidence journal December 2018
Efficacy and safety of a potent new selective cholesterol absorption inhibitor, ezetimibe, in patients with primary hypercholesterolemia journal November 2002
Effectiveness and tolerability of ezetimibe in patients with primary hypercholesterolemia: pooled analysis of two phase II studies journal August 2001
The sterol-sensing domain: multiple families, a unique role? journal April 2002
Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol journal June 2009
Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection journal June 2016
Structural Basis for Cholesterol Transport-like Activity of the Hedgehog Receptor Patched journal November 2018
Crystal Structures of Membrane Transporter MmpL3, an Anti-TB Drug Target journal January 2019
Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins journal October 2019
The Cholesterol Absorption Inhibitor Ezetimibe Acts by Blocking the Sterol-Induced Internalization of NPC1L1 journal June 2008
Inference of Macromolecular Assemblies from Crystalline State journal September 2007
Gctf: Real-time CTF determination and correction journal January 2016
Direct Binding of Cholesterol to the Purified Membrane Region of SCAP journal July 2004
Microscale Fluorescent Thermal Stability Assay for Membrane Proteins journal March 2008
Present status of statin therapy journal April 2015
The Discovery of Ezetimibe:  A View from Outside the Receptor journal January 2004
Crystal structure of bacterial multidrug efflux transporter AcrB journal October 2002
The clathrin adaptor Numb regulates intestinal cholesterol absorption through dynamic interaction with NPC1L1 journal December 2013
Quantifying the local resolution of cryo-EM density maps journal November 2013
Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement journal February 2015
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy journal August 2015
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy journal February 2017
Cellular cholesterol trafficking and compartmentalization journal February 2008
Structures and transport dynamics of a Campylobacter jejuni multidrug efflux pump journal August 2017
PCSK9 inhibitors: clinical evidence and implementation journal November 2018
Structures of human Patched and its complex with native palmitoylated sonic hedgehog journal July 2018
Ezetimibe Added to Statin Therapy after Acute Coronary Syndromes journal June 2015
Binding between the Niemann-Pick C1 protein and a photoactivatable cholesterol analog requires a functional sterol-sensing domain journal August 2004
The target of ezetimibe is Niemann-Pick C1-Like 1 (NPC1L1) journal May 2005
Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels journal January 2006
Extracellular loop C of NPC1L1 is important for binding to ezetimibe journal August 2008
Crystal structures of the Burkholderia multivorans hopanoid transporter HpnN journal June 2017
3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport journal August 2017
The N-terminal Domain of NPC1L1 Protein Binds Cholesterol and Plays Essential Roles in Cholesterol Uptake journal May 2011
Niemann-Pick C1 Like 1 (NPC1L1) Is the Intestinal Phytosterol and Cholesterol Transporter and a Key Modulator of Whole-body Cholesterol Homeostasis journal June 2004
Ezetimibe-sensitive cholesterol uptake by NPC1L1 protein does not require endocytosis journal June 2016
Ezetimibe-sensitive cholesterol uptake by NPC1L1 protein does not require endocytosis journal June 2016
Low-density lipoproteins cause atherosclerotic cardiovascular disease. 1. Evidence from genetic, epidemiologic, and clinical studies. A consensus statement from the European Atherosclerosis Society Consensus Panel journal April 2017
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Features and development of Coot journal March 2010
Disposition of the Selective Cholesterol Absorption Inhibitor Ezetimibe in Healthy Male Subjects journal April 2002
Madin-Darby Canine Kidney II Cells: A Pharmacologically Validated System for NPC1L1-Mediated Cholesterol Uptake journal January 2008
Structural basis of sterol recognition by human hedgehog receptor PTCH1 journal September 2019
Niemann-Pick C1 Like 1 Protein Is Critical for Intestinal Cholesterol Absorption journal February 2004
Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex journal August 2018
Structural basis for the recognition of Sonic Hedgehog by human Patched1 journal June 2018
Heart Disease and Stroke Statistics—2011 Update: A Report From the American Heart Association journal February 2011
Hepatic Niemann-Pick C1–like 1 regulates biliary cholesterol concentration and is a target of ezetimibe journal July 2007
MOLE 2.0: advanced approach for analysis of biomacromolecular channels journal August 2013
Localization and role of NPC1L1 in cholesterol absorption in human intestine journal July 2006
The Structure of the NPC1L1 N-Terminal Domain in a Closed Conformation journal April 2011
Molecular Pathways Underlying Cholesterol Homeostasis journal June 2018
Sampling the conformational space of the catalytic subunit of human γ-secretase journal December 2015
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta journal September 2016
New tools for automated high-resolution cryo-EM structure determination in RELION-3 journal November 2018

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