3GKJ | pdb_00003gkj

NPC1D(NTD):25hydroxycholesterol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3GKJ

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol.

Kwon, H.J.Abi-Mosleh, L.Wang, M.L.Deisenhofer, J.Goldstein, J.L.Brown, M.S.Infante, R.E.

(2009) Cell 137: 1213-1224

  • DOI: https://doi.org/10.1016/j.cell.2009.03.049
  • Primary Citation Related Structures: 
    3GKH, 3GKI, 3GKJ

  • PubMed Abstract: 

    LDL delivers cholesterol to lysosomes by receptor-mediated endocytosis. Exit of cholesterol from lysosomes requires two proteins, membrane-bound Niemann-Pick C1 (NPC1) and soluble NPC2. NPC2 binds cholesterol with its isooctyl side chain buried and its 3beta-hydroxyl exposed. Here, we describe high-resolution structures of the N-terminal domain (NTD) of NPC1 and complexes with cholesterol and 25-hydroxycholesterol. NPC1(NTD) binds cholesterol in an orientation opposite to NPC2: 3beta-hydroxyl buried and isooctyl side chain exposed. Cholesterol transfer from NPC2 to NPC1(NTD) requires reorientation of a helical subdomain in NPC1(NTD), enlarging the opening for cholesterol entry. NPC1 with point mutations in this subdomain (distinct from the binding subdomain) cannot accept cholesterol from NPC2 and cannot restore cholesterol exit from lysosomes in NPC1-deficient cells. We propose a working model wherein after lysosomal hydrolysis of LDL-cholesteryl esters, cholesterol binds NPC2, which transfers it to NPC1(NTD), reversing its orientation and allowing insertion of its isooctyl side chain into the outer lysosomal membranes.


  • Organizational Affiliation
    • Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.

Macromolecule Content 

  • Total Structure Weight: 26.79 kDa 
  • Atom Count: 1,949 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Niemann-Pick C1 protein232Homo sapiensMutation(s): 3 
Gene Names: NPC1
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens)
Explore O15118 
Go to UniProtKB:  O15118
PHAROS:  O15118
GTEx:  ENSG00000141458 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15118
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O15118-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HC3

Query on HC3



Download:Ideal Coordinates CCD File
D [auth A]25-HYDROXYCHOLESTEROL
C27 H46 O2
INBGSXNNRGWLJU-ZHHJOTBYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
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: 1.60 Å
  • R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.926α = 90
b = 65.926β = 90
c = 82.988γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2009-07-14 
  • Deposition Author(s): Kwon, H.J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Data collection, Structure summary