Crystal structure of S. cerevisia Niemann-Pick type C protein NPC2 with ergosterol bound

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 

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Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins.

Winkler, M.B.L.Kidmose, R.T.Szomek, M.Thaysen, K.Rawson, S.Muench, S.P.Wustner, D.Pedersen, B.P.

(2019) Cell 179: 485-497.e18

  • DOI: https://doi.org/10.1016/j.cell.2019.08.038
  • Primary Citation of Related Structures:  
    6R4L, 6R4M, 6R4N

  • PubMed Abstract: 

    Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C.

  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Aarhus C 8000, Denmark. Electronic address: bpp@mbg.au.dk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylglycerol/phosphatidylinositol transfer protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I
201Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NPC2YDL046WD2699
Membrane Entity: Yes 
Find proteins for Q12408 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12408 
Go to UniProtKB:  Q12408
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12408
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ERG

Download Ideal Coordinates CCD File 
L [auth A],
LA [auth I],
R [auth C],
U [auth C],
X [auth E]
C28 H44 O
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth G]
GA [auth H]
K [auth A]
P [auth B]
Q [auth C]
EA [auth G],
GA [auth H],
K [auth A],
P [auth B],
Q [auth C],
V [auth D],
W [auth E],
Z [auth F]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth F]
FA [auth G]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
FA [auth G],
HA [auth H],
IA [auth H],
JA [auth H],
KA [auth I],
M [auth A],
MA [auth I],
N [auth A],
O [auth A],
S [auth C],
T [auth C],
Y [auth E]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.39α = 90
b = 215.39β = 90
c = 129.81γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilDenmark637372
Danish Council for Independent ResearchDenmarkDFF-4002-0052
Other privateDenmarkCarlsberg Foundation CF17-0180
Other privateDenmarkAIAS fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary