3QNT

NPC1L1 (NTD) Structure

• PDB DOI: https://doi.org/10.2210/pdb3QNT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2011-02-09 Released: 2011-05-11 
• Deposition Author(s): Kwon, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.290 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

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

• PubMed: 21525977 
• DOI: https://doi.org/10.1371/journal.pone.0018722
• Primary Citation of Related Structures:  
  3QNT


• 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.52 kDa 
• Atom Count: 1,832 
• Modelled Residue Count: 244 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Niemann-Pick C1-like protein 1	A	265	Homo sapiens	Mutation(s): 0  Gene Names: NPC1L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHC9 (Homo sapiens) Explore Q9UHC9  Go to UniProtKB:  Q9UHC9
PHAROS:  Q9UHC9 GTEx:  ENSG00000015520

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 73.235	α = 90
b = 107.133	β = 90
c = 68.718	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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