8J19

Cryo-EM structure of the LY237-bound GPR84 receptor-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb8J19/pdb
• EM Map EMD-35914: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2023-04-12 Released: 2023-06-21 
• Deposition Author(s): Liu, H., Yin, W., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into ligand recognition and activation of the medium-chain fatty acid-sensing receptor GPR84

Liu, H., Zhang, Q., He, X., Jiang, M., Wang, S., Yan, X., Cheng, X., Liu, Y., Nan, F.J., Xu, H.E., Xie, X., Yin, W.

(2023) Nat Commun 14: 3271

• DOI: https://doi.org/10.1038/s41467-023-38985-6

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 160.61 kDa 
• Atom Count: 8,801 
• Modelled Residue Count: 1,129 
• Deposited Residue Count: 1,448 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 84	A [auth R]	406	Homo sapiens	Mutation(s): 0  Gene Names: GPR84 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS5 (Homo sapiens) Explore Q9NQS5  Go to UniProtKB:  Q9NQS5
PHAROS:  Q9NQS5 GTEx:  ENSG00000139572

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B [auth A]	354	Homo sapiens	Mutation(s): 4  Gene Names: GNAI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

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]	348	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
Antibody fragment ScFv16	D [auth S]	269	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SWO (Subject of Investigation/LOI)	F [auth R]	6-nonylpyridine-2,4-diol C14 H23 N O2 JCINCSYDDSRQQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Liu, H., Yin, W., Xu, H.E.

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

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2023-07-05
  Changes: Database references