7TD4

Sphingosine-1-phosphate receptor 1-Gi complex bound to Siponimod


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Differential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate.

Liu, S.Paknejad, N.Zhu, L.Kihara, Y.Ray, M.Chun, J.Liu, W.Hite, R.K.Huang, X.Y.

(2022) Nat Commun 13: 731-731

  • DOI: https://doi.org/10.1038/s41467-022-28417-2
  • Primary Citation of Related Structures:  
    7TD0, 7TD1, 7TD2, 7TD3, 7TD4

  • PubMed Abstract: 

    Lysophospholipids are bioactive lipids and can signal through G-protein-coupled receptors (GPCRs). The best studied lysophospholipids are lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P). The mechanisms of lysophospholipid recognition by an active GPCR, and the activations of lysophospholipid GPCR-G-protein complexes remain unclear. Here we report single-particle cryo-EM structures of human S1P receptor 1 (S1P 1 ) and heterotrimeric G i complexes formed with bound S1P or the multiple sclerosis (MS) treatment drug Siponimod, as well as human LPA receptor 1 (LPA 1 ) and G i complexes in the presence of LPA. Our structural and functional data provide insights into how LPA and S1P adopt different conformations to interact with their cognate GPCRs, the selectivity of the homologous lipid GPCRs for S1P versus LPA, and the different activation mechanisms of these GPCRs by LPA and S1P. Our studies also reveal specific optimization strategies to improve the MS-treating S1P 1 -targeting drugs.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]340Bos taurusMutation(s): 0 
Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus)
Explore P62871 
Go to UniProtKB:  P62871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62871
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]379Rattus norvegicusMutation(s): 1 
Gene Names: Gnai1Gnai-1
EC: 3.6.5
Membrane Entity: Yes 
UniProt
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10824
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Bos taurusMutation(s): 1 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt
Find proteins for P63212 (Bos taurus)
Explore P63212 
Go to UniProtKB:  P63212
Entity Groups  
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UniProt GroupP63212
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine 1-phosphate receptor 1D [auth R]392Homo sapiensMutation(s): 0 
Gene Names: S1PR1CHEDG1EDG1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21453 (Homo sapiens)
Explore P21453 
Go to UniProtKB:  P21453
PHAROS:  P21453
GTEx:  ENSG00000170989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21453
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P21453-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J8C (Subject of Investigation/LOI)
Query on J8C

Download Ideal Coordinates CCD File 
F [auth R]1-[[4-[(~{E})-~{N}-[[4-cyclohexyl-3-(trifluoromethyl)phenyl]methoxy]-~{C}-methyl-carbonimidoyl]-2-ethyl-phenyl]methyl]azetidine-3-carboxylic acid
C29 H35 F3 N2 O3
KIHYPELVXPAIDH-HNSNBQBZSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth R]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J8C BindingDB:  7TD4 EC50: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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 StatesGM138676
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM132307
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA243235

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary