8U8F

GPR3 Orphan G-coupled Protein Receptor in complex with Dominant Negative Gs.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lipid-Dependent Activation of the Orphan G Protein-Coupled Receptor, GPR3.

Russell, I.C.Zhang, X.Bumbak, F.McNeill, S.M.Josephs, T.M.Leeming, M.G.Christopoulos, G.Venugopal, H.Flocco, M.M.Sexton, P.M.Wootten, D.Belousoff, M.J.

(2024) Biochemistry 63: 625-631

  • DOI: https://doi.org/10.1021/acs.biochem.3c00647
  • Primary Citation of Related Structures:  
    8U8F

  • PubMed Abstract: 

    The class A orphan G protein-coupled receptor (GPCR), GPR3, has been implicated in a variety of conditions, including Alzheimer's and premature ovarian failure. GPR3 constitutively couples with Gαs, resulting in the production of cAMP in cells. While tool compounds and several putative endogenous ligands have emerged for the receptor, its endogenous ligand, if it exists, remains a mystery. As novel potential drug targets, the structures of orphan GPCRs have been of increasing interest, revealing distinct modes of activation, including autoactivation, presence of constitutively activating mutations, or via cryptic ligands. Here, we present a cryo-electron microscopy (cryo-EM) structure of the orphan GPCR, GPR3 in complex with DNGαs and Gβ 1 γ 2 . The structure revealed clear density for a lipid-like ligand that bound within an extended hydrophobic groove, suggesting that the observed "constitutive activity" was likely due to activation via a lipid that may be ubiquitously present. Analysis of conformational variance within the cryo-EM data set revealed twisting motions of the GPR3 transmembrane helices that appeared coordinated with changes in the lipid-like density. We propose a mechanism for the binding of a lipid to its putative orthosteric binding pocket linked to the GPR3 dynamics.


  • Organizational Affiliation

    Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short394Homo sapiensMutation(s): 0 
Gene Names: GNASGNAS1GSP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Homo sapiensMutation(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 
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UniProt GroupP62873
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]58Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 3D [auth R]390Homo sapiensMutation(s): 0 
Gene Names: GPR3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P46089 (Homo sapiens)
Explore P46089 
Go to UniProtKB:  P46089
PHAROS:  P46089
GTEx:  ENSG00000181773 
Entity Groups  
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UniProt GroupP46089
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
E [auth R]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1150083
Australian Research Council (ARC)AustraliaIC200100052
National Health and Medical Research Council (NHMRC, Australia)Australia1154434
National Health and Medical Research Council (NHMRC, Australia)Australia1155302

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references