5KWY

Structure of human NPC1 middle lumenal domain bound to NPC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2.

Li, X.Saha, P.Li, J.Blobel, G.Pfeffer, S.R.

(2016) Proc.Natl.Acad.Sci.USA 113: 10079-10084

  • DOI: 10.1073/pnas.1611956113

  • PubMed Abstract: 
  • Export of LDL-derived cholesterol from lysosomes requires the cooperation of the integral membrane protein Niemann-Pick C1 (NPC1) and a soluble protein, Niemann-Pick C2 (NPC2). Mutations in the genes encoding these proteins lead to Niemann-Pick disea ...

    Export of LDL-derived cholesterol from lysosomes requires the cooperation of the integral membrane protein Niemann-Pick C1 (NPC1) and a soluble protein, Niemann-Pick C2 (NPC2). Mutations in the genes encoding these proteins lead to Niemann-Pick disease type C (NPC). NPC2 binds to NPC1's second (middle), lumenally oriented domain (MLD) and transfers cholesterol to NPC1's N-terminal domain (NTD). Here, we report the 2.4-Å resolution crystal structure of a complex of human NPC1-MLD and NPC2 bearing bound cholesterol-3-O-sulfate. NPC1-MLD uses two protruding loops to bind NPC2, analogous to its interaction with the primed Ebola virus glycoprotein. Docking of the NPC1-NPC2 complex onto the full-length NPC1 structure reveals a direct cholesterol transfer tunnel between NPC2 and NTD cholesterol binding pockets, supporting the "hydrophobic hand-off" cholesterol transfer model.


    Organizational Affiliation

    Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065; xli05@rockefeller.edu blobel@rockefeller.edu pfeffer@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Niemann-Pick C1 protein
A, B
247Homo sapiensGene Names: NPC1
Find proteins for O15118 (Homo sapiens)
Go to Gene View: NPC1
Go to UniProtKB:  O15118
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Epididymal secretory protein E1
C, D
133Homo sapiensGene Names: NPC2 (HE1)
Find proteins for P61916 (Homo sapiens)
Go to Gene View: NPC2
Go to UniProtKB:  P61916
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3S
Query on C3S

Download SDF File 
Download CCD File 
C, D
CHOLEST-5-EN-3-YL HYDROGEN SULFATE
CHOLESTEROL-SULFATE
C27 H46 O4 S
BHYOQNUELFTYRT-DPAQBDIFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.956α = 90.00
b = 109.686β = 90.00
c = 154.560γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-19 
  • Released Date: 2016-08-24 
  • Deposition Author(s): Li, X.

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2016-09-14
    Type: Database references