8G92

Structure of inhibitor 16d-bound SPNS2

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMMemProtMD

  • Deposited: 2023-02-21 Released: 2023-05-24 
  • Deposition Author(s): Chen, H., Li, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Damon Runyon Cancer Research Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional insights into Spns2-mediated transport of sphingosine-1-phosphate.

Chen, H.Ahmed, S.Zhao, H.Elghobashi-Meinhardt, N.Dai, Y.Kim, J.H.McDonald, J.G.Li, X.Lee, C.H.

(2023) Cell 186: 2644-2655.e16

  • DOI: https://doi.org/10.1016/j.cell.2023.04.028
  • Primary Citation of Related Structures:  
    8EX4, 8EX5, 8EX6, 8EX7, 8EX8, 8G92

  • PubMed Abstract: 

    Sphingosine-1-phosphate (S1P) is an important signaling sphingolipid that regulates the immune system, angiogenesis, auditory function, and epithelial and endothelial barrier integrity. Spinster homolog 2 (Spns2) is an S1P transporter that exports S1P to initiate lipid signaling cascades. Modulating Spns2 activity can be beneficial in treatments of cancer, inflammation, and immune diseases. However, the transport mechanism of Spns2 and its inhibition remain unclear. Here, we present six cryo-EM structures of human Spns2 in lipid nanodiscs, including two functionally relevant intermediate conformations that link the inward- and outward-facing states, to reveal the structural basis of the S1P transport cycle. Functional analyses suggest that Spns2 exports S1P via facilitated diffusion, a mechanism distinct from other MFS lipid transporters. Finally, we show that the Spns2 inhibitor 16d attenuates the transport activity by locking Spns2 in the inward-facing state. Our work sheds light on Spns2-mediated S1P transport and aids the development of advanced Spns2 inhibitors.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine-1-phosphate transporter SPNS2458Homo sapiensMutation(s): 0 
Gene Names: SPNS2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVW8 (Homo sapiens)
Explore Q8IVW8 
Go to UniProtKB:  Q8IVW8
PHAROS:  Q8IVW8
GTEx:  ENSG00000183018 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVW8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YUX (Subject of Investigation/LOI)
Query on YUX

Download Ideal Coordinates CCD File 
B [auth A]3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine
C21 H33 N3 O
VLTITRMWGPJCFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM135343
Welch FoundationUnited StatesI-1957
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01 HL160487-01
Damon Runyon Cancer Research FoundationUnited StatesDRR-53S-19

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references