5U73

Crystal structure of human Niemann-Pick C1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.348 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

3.3 angstrom structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport.

Li, X.Lu, F.Trinh, M.N.Schmiege, P.Seemann, J.Wang, J.Blobel, G.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 9116-9121

  • DOI: 10.1073/pnas.1711716114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Niemann-Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann-Pick type C disease, a lysosomal storage disease. Despite recent reports of the NP ...

    Niemann-Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann-Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314-1,278), which-in contrast to previous lower resolution structures-features the entire CTD well resolved. Notably, all eight cysteines of the CTD form four disulfide bonds, one of which (C909-C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD-NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.


    Organizational Affiliation

    Laboratory of Cell Biology, The Rockefeller University, New York, NY 10065; xli05@rockefeller.edu blobel@rockefeller.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Niemann-Pick C1 protein
A
1278Homo sapiensMutation(s): 0 
Gene Names: NPC1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sterol-Sensing Domain (SSD) Proteins
Protein: 
Niemann-Pick C1 protein (NPC1*)
Find proteins for O15118 (Homo sapiens)
Go to Gene View: NPC1
Go to UniProtKB:  O15118
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.348 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 181.937α = 90.00
b = 223.071β = 105.31
c = 63.208γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Advisory, Structure summary