7EW2 | pdb_00007ew2

Cryo-EM structure of pFTY720-bound Sphingosine 1-phosphate receptor 3 in complex with Gi protein

• PDB DOI: https://doi.org/10.2210/pdb7EW2/pdb
• EM Map EMD-31345: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-05-24 Released: 2021-09-29 
• Deposition Author(s): Zhao, C., Wang, W., Wang, H.L., Shao, Z.H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into sphingosine-1-phosphate recognition and ligand selectivity of S1PR3-Gi signaling complexes.

Zhao, C., Cheng, L., Wang, W., Wang, H., Luo, Y., Feng, Y., Wang, X., Fu, H., Cai, Y., Yang, S., Fu, P., Yan, W., Shao, Z.

(2022) Cell Res 32: 218-221

• PubMed: 34545189 
• DOI: https://doi.org/10.1038/s41422-021-00567-w
• Primary Citation Related Structures: 
  7EW2, 7EW3, 7EW4

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Organizational Affiliation: 
• Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].
Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 162.88 kDa 
• Atom Count: 9,001 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,459 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	356	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFV16	D [auth S]	266	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 3	E [auth R]	412	Homo sapiens	Mutation(s): 0  Gene Names: S1PR3, EDG3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99500 (Homo sapiens) Explore Q99500  Go to UniProtKB:  Q99500
PHAROS:  Q99500 GTEx:  ENSG00000213694

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J89 (Subject of Investigation/LOI)	F [auth R]	(2~{S})-2-azanyl-4-(4-octylphenyl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]butan-1-ol C19 H34 N O5 P LRFKWQGGENFBFO-IBGZPJMESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J89	BindingDB:  7EW2	Ki: 5.9 (nM) from 1 assay(s)
		IC50: min: 6.3, max: 23 (nM) from 2 assay(s)
		EC50: min: 0.13, max: 94 (nM) from 11 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Zhao, C., Wang, W., Wang, H.L., Shao, Z.H.

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection