8YIC | pdb_00008yic

SAR247799-bound S1PR1-Gi protein complex

• PDB DOI: https://doi.org/10.2210/pdb8YIC/pdb
• EM Map EMD-39313: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-02-29 Released: 2024-12-11 
• Deposition Author(s): Xu, Z., Yu, J.J., Shao, Z.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SAR247799-bound S1PR1 in complex with Gi heterotrimer

Xu, Z., Yu, J.J., Wang, K.X., Yan, W., Shao, Z.H.

To be published.

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: 145.92 kDa 
• Atom Count: 7,307 
• Modeled Residue Count: 923 
• Deposited Residue Count: 1,293 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	364	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	343	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
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
Endolysin,Sphingosine 1-phosphate receptor 1	D [auth R]	515	Tequatrovirus T4, Homo sapiens This entity is chimeric	Mutation(s): 5  Gene Names: E, S1PR1, CHEDG1, EDG1 EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P21453 (Homo sapiens) Explore P21453  Go to UniProtKB:  P21453
PHAROS:  P21453 GTEx:  ENSG00000170989
UniProt Groups	P00720P21453

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LYQ (Subject of Investigation/LOI)	E [auth R]	SAR247799 C21 H16 Cl N3 O5 WRBZNIUFAKIIQG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Xu, Z., Yu, J.J., Shao, Z.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270438
National Natural Science Foundation of China (NSFC)	China	32170498
National Natural Science Foundation of China (NSFC)	China	32371288

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection