8G05

Cryo-EM structure of an orphan GPCR-Gi protein signaling complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Pro-phagocytic function and structural basis of GPR84 signaling.

Zhang, X.Wang, Y.Supekar, S.Cao, X.Zhou, J.Dang, J.Chen, S.Jenkins, L.Marsango, S.Li, X.Liu, G.Milligan, G.Feng, M.Fan, H.Gong, W.Zhang, C.

(2023) Nat Commun 14: 5706-5706

  • DOI: https://doi.org/10.1038/s41467-023-41201-0
  • Primary Citation of Related Structures:  
    8G05

  • PubMed Abstract: 

    GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance phagocytic activities of macrophages. In this study, we show that the activation of GPR84 by the synthetic agonist 6-OAU can synergize with the blockade of CD47 on cancer cells to induce phagocytosis of cancer cells by macrophages. We also determine a high-resolution structure of the GPR84-G i signaling complex with 6-OAU. This structure reveals an occluded binding pocket for 6-OAU, the molecular basis of receptor activation involving non-conserved structural motifs of GPR84, and an unusual G i -coupling interface. Together with computational docking and simulations studies, this structure also suggests a mechanism for the high selectivity of GPR84 for MCFAs and a potential routes of ligand binding and dissociation. These results provide a framework for understanding GPR84 signaling and developing new drugs targeting GPR84.


  • Organizational Affiliation

    Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 84A [auth R]440Homo sapiensMutation(s): 0 
Gene Names: GPR84EX33
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQS5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]376Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth E]266Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
G [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
YI9 (Subject of Investigation/LOI)
Query on YI9

Download Ideal Coordinates CCD File 
F [auth R]6-(octylamino)pyrimidine-2,4(3H,5H)-dione
C12 H21 N3 O2
PNPWQWFLXGGIRQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128641
Ministry of Science and Technology (MoST, China)China2019YFA0904100
National Natural Science Foundation of China (NSFC)ChinaT2221005

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release