9VNY | pdb_00009vny

Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CYM5442

• PDB DOI: https://doi.org/10.2210/pdb9VNY/pdb
• EM Map EMD-65218: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Escherichia coli
• Expression System: Spodoptera frugiperda, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-07-01 Released: 2026-01-28 
• Deposition Author(s): Yu, L.Y., Jiao, H.Z., Ti, R.J., Pang, B., Gan, B., Ren, R.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Gi coupled Sphingosine 1-phosphate receptor bound with CYM5442

Yu, L.Y., Jiao, H.Z., Ti, R.J., Pang, B., Gan, B., Ren, R.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 174.74 kDa 
• Atom Count: 8,873 
• Modeled Residue Count: 1,137 
• Deposited Residue Count: 1,567 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A	357	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth D]	354	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	251	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Sphingosine 1-phosphate receptor 1	E [auth F]	534	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: cybC, S1PR1, CHEDG1, EDG1
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P21453 (Homo sapiens) Explore P21453  Go to UniProtKB:  P21453
PHAROS:  P21453 GTEx:  ENSG00000170989
UniProt Groups	P0ABE7P21453

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L3G (Subject of Investigation/LOI)	F	2-[[(1~{R})-4-[5-(3,4-diethoxyphenyl)-1,2,4-oxadiazol-3-yl]-2,3-dihydro-1~{H}-inden-1-yl]amino]ethanol C23 H27 N3 O4 NUIKTBLZSPQGCP-LJQANCHMSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Yu, L.Y., Jiao, H.Z., Ti, R.J., Pang, B., Gan, B., Ren, R.B.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release