8QV5 | pdb_00008qv5

Structure of human SPNS2 in LMNG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2.

Li, H.Z.Pike, A.C.W.Chang, Y.N.Prakaash, D.Gelova, Z.Stanka, J.Moreau, C.Scott, H.C.Wunder, F.Wolf, G.Scacioc, A.McKinley, G.Batoulis, H.Mukhopadhyay, S.Garofoli, A.Pinto-Fernandez, A.Kessler, B.M.Burgess-Brown, N.A.Stefanic, S.Wiedmer, T.Durr, K.L.Puetter, V.Ehrmann, A.Khalid, S.Ingles-Prieto, A.Superti-Furga, G.Sauer, D.B.

(2025) Nat Commun 16: 721-721

  • DOI: https://doi.org/10.1038/s41467-025-55942-7
  • Primary Citation of Related Structures:  
    8QV5, 8QV6

  • PubMed Abstract: 

    Sphingosine-1-phosphate (S1P) is a signaling lysolipid critical to heart development, immunity, and hearing. Accordingly, mutations in the S1P transporter SPNS2 are associated with reduced white cell count and hearing defects. SPNS2 also exports the S1P-mimicking FTY720-P (Fingolimod) and thereby is central to the pharmacokinetics of this drug when treating multiple sclerosis. Here, we use a combination of cryo-electron microscopy, immunofluorescence, in vitro binding and in vivo S1P export assays, and molecular dynamics simulations to probe SPNS2's substrate binding and transport. These results reveal the transporter's binding mode to its native substrate S1P, the therapeutic FTY720-P, and the reported SPNS2-targeting inhibitor 33p. Further capturing an inward-facing apo state, our structures illuminate the protein's mechanism for exchange between inward-facing and outward-facing conformations. Finally, using these structural, localization, and S1P transport results, we identify how pathogenic mutations ablate the protein's export activity and thereby lead to hearing loss.


  • Organizational Affiliation
    • Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine-1-phosphate transporter SPNS2556Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody D12143Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20_4459

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeSwitzerland777372
Wellcome TrustUnited Kingdom106169/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release