9WIK | pdb_00009wik

Cryo-EM structure of GPR84-Gi complex with DL-175

• PDB DOI: https://doi.org/10.2210/pdb9WIK/pdb
• EM Map EMD-65999: EMDB EMDataResource

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


• Deposited: 2025-08-28 Released: 2026-07-01 
• Deposition Author(s): Suzuki, S., Nishikawa, K., Tran, D.P., Akio, K., Fujiyoshi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanistic insight into signal bias by the agonist-dependent conformational dynamics of GPR84

Suzuki, S., Nishikawa, K., Tran, D.P., Akio, K., Fujiyoshi, Y.

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: 193.42 kDa 
• Atom Count: 8,711 
• Modeled Residue Count: 1,121 
• Deposited Residue Count: 1,745 
• 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): 4  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	382	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	70	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
Soluble cytochrome b562,G-protein coupled receptor 84,LgBiT tag	D [auth R]	691	Escherichia coli, Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 0  Gene Names: cybC, GPR84, EX33
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9NQS5 (Homo sapiens) Explore Q9NQS5  Go to UniProtKB:  Q9NQS5
PHAROS:  Q9NQS5 GTEx:  ENSG00000139572
UniProt Groups	Q9NQS5P0ABE7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv16	E [auth S]	248	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1MBR( Subject of Investigation/LOI)	F [auth R]	3-[2-(4-chloranylnaphthalen-1-yl)oxyethyl]-1-oxidanidyl-pyridin-1-ium C17 H14 Cl N O2 FXOVKEUUTXBOJZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Suzuki, S., Nishikawa, K., Tran, D.P., Akio, K., Fujiyoshi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K18061
Japan Society for the Promotion of Science (JSPS)	Japan	20H00451

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release