8KH4

Cryo-EM structure of the GPR161-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive G s signaling.

Nie, Y.Qiu, Z.Chen, S.Chen, Z.Song, X.Ma, Y.Huang, N.Cyster, J.G.Zheng, S.

(2023) Nat Commun 14: 5901-5901

  • DOI: https://doi.org/10.1038/s41467-023-41654-3
  • Primary Citation of Related Structures:  
    8KGK, 8KH4, 8KH5

  • PubMed Abstract: 

    Many orphan G protein-coupled receptors (GPCRs) remain understudied because their endogenous ligands are unknown. Here, we show that a group of class A/rhodopsin-like orphan GPCRs including GPR61, GPR161 and GPR174 increase the cAMP level similarly to fully activated D1 dopamine receptor (D1R). We report cryo-electron microscopy structures of the GPR61‒G s , GPR161‒G s and GPR174‒G s complexes without any exogenous ligands. The GPR174 structure reveals that endogenous lysophosphatidylserine (lysoPS) is copurified. While GPR174 fails to respond to exogenous lysoPS, likely owing to its maximal activation by the endogenous ligand, GPR174 mutants with lower ligand binding affinities can be specifically activated by lysoPS but not other lipids, in a dose-dependent manner. Moreover, GPR174 adopts a non-canonical G s coupling mode. The structures of GPR161 and GPR61 reveal that the second extracellular loop (ECL2) penetrates into the orthosteric pocket, possibly contributing to constitutive activity. Our work definitively confirms lysoPS as an endogenous GPR174 ligand and suggests that high constitutive activity of some orphan GPCRs could be accounted for by their having naturally abundant ligands.


  • Organizational Affiliation

    College of Life Sciences, Beijing Normal University, 100875, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 161373Homo sapiensMutation(s): 0 
Gene Names: GPR161
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6U8 (Homo sapiens)
Explore Q8N6U8 
Go to UniProtKB:  Q8N6U8
PHAROS:  Q8N6U8
GTEx:  ENSG00000143147 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N6U8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short249Homo sapiensMutation(s): 16 
Gene Names: GNALGNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P38405 (Homo sapiens)
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Go to UniProtKB:  P38405
PHAROS:  P38405
GTEx:  ENSG00000141404 
Find proteins for P63092 (Homo sapiens)
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Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupsP38405P63092
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1357Homo 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
Nanobody 35D [auth E]160Lama glamaMutation(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 D]71Homo sapiensMutation(s): 1 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release