NPC1L1 (NTD) Structure

Experimental Data Snapshot

  • Resolution: 2.83 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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This is version 1.2 of the entry. See complete history


The Structure of the NPC1L1 N-Terminal Domain in a Closed Conformation.

Kwon, H.J.Palnitkar, M.Deisenhofer, J.

(2011) PLoS One 6: e18722-e18722

  • DOI: https://doi.org/10.1371/journal.pone.0018722
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    NPC1L1 is the molecular target of the cholesterol lowering drug Ezetimibe and mediates the intestinal absorption of cholesterol. Inhibition or deletion of NPC1L1 reduces intestinal cholesterol absorption, resulting in reduction of plasma cholesterol levels. Here we present the 2.8 Å crystal structure of the N-terminal domain (NTD) of NPC1L1 in the absence of cholesterol. The structure, combined with biochemical data, reveals the mechanism of cholesterol selectivity of NPC1L1. Comparison to the cholesterol free and bound structures of NPC1(NTD) reveals that NPC1L1(NTD) is in a closed conformation and the sterol binding pocket is occluded from solvent. The structure of NPC1L1(NTD) reveals a degree of flexibility surrounding the entrance to the sterol binding pocket, suggesting a gating mechanism that relies on multiple movements around the entrance to the sterol binding pocket.

  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America. hyockjoo.kwon@gmail.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Niemann-Pick C1-like protein 1265Homo sapiensMutation(s): 0 
Gene Names: NPC1L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHC9 (Homo sapiens)
Explore Q9UHC9 
Go to UniProtKB:  Q9UHC9
GTEx:  ENSG00000015520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHC9
Glycosylation Sites: 2Go to GlyGen: Q9UHC9-1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.83 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.235α = 90
b = 107.133β = 90
c = 68.718γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2011-05-11 
  • Deposition Author(s): Kwon, H.J.

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary