7T6B

Structure of S1PR2-heterotrimeric G13 signaling complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.19 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

Structure of S1PR2-heterotrimeric G 13 signaling complex.

Chen, H.Chen, K.Huang, W.Staudt, L.M.Cyster, J.G.Li, X.

(2022) Sci Adv 8: eabn0067-eabn0067

  • DOI: https://doi.org/10.1126/sciadv.abn0067
  • Primary Citation of Related Structures:  
    7T6B

  • PubMed Abstract: 

    Sphingosine-1-phosphate (S1P) regulates immune cell trafficking, angiogenesis, and vascular function via its five receptors. Inherited mutations in S1P receptor 2 (S1PR2) occur in individuals with hearing loss, and acquired mutations in S1PR2 and G α13 occur in a malignant lymphoma. Here, we present the cryo-electron microscopy structure of S1P-bound S1PR2 coupled to the heterotrimeric G 13 . Interaction between S1PR2 intracellular loop 2 (ICL2) and transmembrane helix 4 confines ICL2 to engage the α5 helix of G α13 . Transforming growth factor-α shedding assays and cell migration assays support the key roles of the residues in S1PR2-G α13 complex assembly. The structure illuminates the mechanism of receptor disruption by disease-associated mutations. Unexpectedly, we showed that FTY720-P, an agonist of the other four S1PRs, can trigger G 13 activation via S1PR2. S1PR2 F274I variant can increase the activity of G 13 considerably with FTY720-P and S1P, thus revealing a basis for S1PR drug selectivity.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit alpha-13362Homo sapiensMutation(s): 0 
Gene Names: GNA13
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
Find proteins for Q14344 (Homo sapiens)
Explore Q14344 
Go to UniProtKB:  Q14344
PHAROS:  Q14344
GTEx:  ENSG00000120063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63096Q14344
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B [auth C]362Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth D]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth E]259Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingosine 1-phosphate receptor 2E [auth R]361Homo sapiensMutation(s): 0 
Gene Names: S1PR2EDG5
Membrane Entity: Yes 
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Find proteins for O95136 (Homo sapiens)
Explore O95136 
Go to UniProtKB:  O95136
PHAROS:  O95136
GTEx:  ENSG00000267534 
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UniProt GroupO95136
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  • 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 
F [auth R](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: 3.19 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 Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesP01HL020948
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM135343
Damon Runyon Cancer Research FoundationUnited StatesDRR-53S-19

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references