8EX6

Human S1P transporter Spns2 in an inward-facing open conformation (state 1*)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • 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 SPNS2451Homo 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
S1P (Subject of Investigation/LOI)
Query on S1P

Download Ideal Coordinates CCD File 
B [auth A](2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C18 H38 N O5 P
DUYSYHSSBDVJSM-KRWOKUGFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM143282

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection