9VJ6 | pdb_00009vj6

Cryo-EM structure of 5-HT1AR-Gi3 in complex with F-15599

• PDB DOI: https://doi.org/10.2210/pdb9VJ6/pdb
• EM Map EMD-65105: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-06-19 Released: 2025-11-12 
• Deposition Author(s): Wang, C., Cao, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.62 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Pathway-Selective 5-HT1AR Agonist as a Rapid Antidepressant Strategy

Wang, C., Cao, C.

(2025) Cell 

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: 177.59 kDa 
• Atom Count: 8,818 
• Modeled Residue Count: 1,124 
• Deposited Residue Count: 1,583 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-3	A [auth B]	354	Homo sapiens	Mutation(s): 1  Gene Names: GNAI3
UniProt & NIH Common Fund Data Resources
Find proteins for P08754 (Homo sapiens) Explore P08754  Go to UniProtKB:  P08754
PHAROS:  P08754 GTEx:  ENSG00000065135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B [auth C]	358	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 [auth D]	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
ScFv16	D [auth E]	251	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A	E [auth R]	549	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: cybC, HTR1A, ADRB2RL1, ADRBRL1
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens) Explore P08908  Go to UniProtKB:  P08908
PHAROS:  P08908 GTEx:  ENSG00000178394
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	P0ABE7P08908

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T7M	I [auth R]	(2R)-1-(heptadecanoyloxy)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate C46 H82 O16 P2 WSLBJQQQZZTFBA-NPJVAJNNSA-N
A1ESC (Subject of Investigation/LOI)	F [auth R]	(3-chloranyl-4-fluoranyl-phenyl)-[4-fluoranyl-4-[[(5-methylpyrimidin-2-yl)methylamino]methyl]piperidin-1-yl]methanone C19 H21 Cl F2 N4 O WAAXKNFGOFTGLP-UHFFFAOYSA-N
CLR	G [auth R], H [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.62 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.41

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Wang, C., Cao, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	GG9100007022

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release