7EJX | pdb_00007ejx

Structure of the GPR88-Gi1 signaling complex bound to a synthetic ligand


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7EJX

This is version 2.2 of the entry. See complete history

Literature

Activation and allosteric regulation of the orphan GPR88-Gi1 signaling complex.

Chen, G.Xu, J.Inoue, A.Schmidt, M.F.Bai, C.Lu, Q.Gmeiner, P.Liu, Z.Du, Y.

(2022) Nat Commun 13: 2375-2375

  • DOI: https://doi.org/10.1038/s41467-022-30081-5
  • Primary Citation Related Structures: 
    7EJX, 7WZ4

  • PubMed Abstract: 

    GPR88 is an orphan class A G-protein-coupled receptor that is highly expressed in the striatum and regulates diverse brain and behavioral functions. Here we present cryo-EM structures of the human GPR88-Gi1 signaling complex with or without a synthetic agonist (1R, 2R)-2-PCCA. We show that (1R, 2R)-2-PCCA is an allosteric modulator binding to a herein identified pocket formed by the cytoplasmic ends of transmembrane segments 5, 6, and the extreme C terminus of the α5 helix of Gi1. We also identify an electron density in the extracellular orthosteric site that may represent a putative endogenous ligand of GPR88. These structures, together with mutagenesis studies and an inactive state model obtained from metadynamics simulations, reveal a unique activation mechanism for GPR88 with a set of distinctive structure features and a water-mediated polar network. Overall, our results provide a structural framework for understanding the ligand binding, activation and signaling mechanism of GPR88, and will facilitate the innovative drug discovery for neuropsychiatric disorders and for deorphanization of this receptor.


  • Organizational Affiliation
    • Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China.

Macromolecule Content 

  • Total Structure Weight: 157.26 kDa 
  • Atom Count: 8,334 
  • Modeled Residue Count: 1,071 
  • Deposited Residue Count: 1,425 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable G-protein coupled receptor 88A [auth R]384Homo sapiensMutation(s): 1 
Gene Names: GPR88STRG
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZN0 (Homo sapiens)
Explore Q9GZN0 
Go to UniProtKB:  Q9GZN0
PHAROS:  Q9GZN0
GTEx:  ENSG00000181656 
Entity Groups
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UniProt GroupQ9GZN0
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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): 0 
Gene Names: GNAI1
EC: 3.6.5
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 Groups
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UniProt GroupP63096
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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(T) subunit beta-1C [auth B]357Homo 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 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(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 
Entity Groups
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16E [auth S]259Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 2.0: 2022-04-27
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-10-26
    Changes: Database references
  • Version 2.2: 2024-11-13
    Changes: Data collection, Structure summary