9W0M | pdb_00009w0m

Cryo-EM structure of S1P2 in complex with heterotrimeric G protein

• PDB DOI: https://doi.org/10.2210/pdb9W0M/pdb
• EM Map EMD-65508: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-07-24 Released: 2026-06-03 
• Deposition Author(s): Wu, B., Zhao, Q., Tan, Q.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis of allosteric and bitopic ligands binding in sphingosine-1-phosphate receptors 2 and 3.

Wu, Y., Chen, Q., Wang, H., Liu, K., Wei, J., Wang, M., Chen, K., Zhu, Y., Han, S., Yi, C., Ma, L., Schnapp, G., Pautsch, A., Gnamm, C., Grauert, M., Schmidt, E., Tan, Q., Wu, B., Zhao, Q.

(2025) Protein Cell 

• PubMed: 40851516 
• DOI: https://doi.org/10.1093/procel/pwaf068
• Primary Citation Related Structures: 
  9W0H, 9W0L, 9W0M, 9W0O

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Organizational Affiliation: 
• State Key Laboratory of Drug Research and State Key Laboratory of Chemistry Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
University of Chinese Academy of Sciences, Beijing 100864, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
Lingang Laboratory, Shanghai 200031, China.
Boehringer-Ingelheim Pharma GmbH & Co. KG, Department of Medicinal Chemistry, Biberach 88397, Germany.
Boehringer-Ingelheim Pharma GmbH & Co. KG, Department of Drug Discovery Sciences, Biberach 88397, Germany.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
Zhongshan Institute of Drug Discovery, SIMM, CAS, Zhongshan 528400, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 129.78 kDa 
• Atom Count: 6,881 
• Modeled Residue Count: 888 
• Deposited Residue Count: 1,164 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 2	A	405	Homo sapiens	Mutation(s): 0  Gene Names: S1PR2, EDG5
UniProt & NIH Common Fund Data Resources
Find proteins for O95136 (Homo sapiens) Explore O95136  Go to UniProtKB:  O95136
PHAROS:  O95136 GTEx:  ENSG00000267534

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth C]	54	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	351	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	D	354	Homo sapiens	Mutation(s): 5  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Wu, B., Zhao, Q., Tan, Q.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2022YFA1302900
National Science Foundation (NSF, China)	China	82121005
National Science Foundation (NSF, China)	China	XDB37030100

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release