8H8J | pdb_00008h8j

Lodoxamide-bound GPR35 in complex with G13


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into divalent cation regulation and G 13 -coupling of orphan receptor GPR35.

Duan, J.Liu, Q.Yuan, Q.Ji, Y.Zhu, S.Tan, Y.He, X.Xu, Y.Shi, J.Cheng, X.Jiang, H.Eric Xu, H.Jiang, Y.

(2022) Cell Discov 8: 135-135

  • DOI: https://doi.org/10.1038/s41421-022-00499-8
  • Primary Citation of Related Structures:  
    8H8J

  • PubMed Abstract: 

    Endogenous ions play important roles in the function and pharmacology of G protein-coupled receptors (GPCRs) with limited atomic evidence. In addition, compared with G protein subtypes G s , G i/o , and G q/11 , insufficient structural evidence is accessible to understand the coupling mechanism of G 12/13 protein by GPCRs. Orphan receptor GPR35, which is predominantly expressed in the gastrointestinal tract and is closely related to inflammatory bowel diseases (IBDs), stands out as a prototypical receptor for investigating ionic modulation and G 13 coupling. Here we report a cryo-electron microscopy structure of G 13 -coupled GPR35 bound to an anti-allergic drug, lodoxamide. This structure reveals a novel divalent cation coordination site and a unique ionic regulatory mode of GPR35 and also presents a highly positively charged binding pocket and the complementary electrostatic ligand recognition mode, which explain the promiscuity of acidic ligand binding by GPR35. Structural comparison of the GPR35-G 13 complex with other G protein subtypes-coupled GPCRs reveals a notable movement of the C-terminus of α5 helix of the Gα 13 subunit towards the receptor core and the least outward displacement of the cytoplasmic end of GPR35 TM6. A featured 'methionine pocket' contributes to the G 13 coupling by GPR35. Together, our findings provide a structural basis for divalent cation modulation, ligand recognition, and subsequent G 13 protein coupling of GPR35 and offer a new opportunity for designing GPR35-targeted drugs for the treatment of IBDs.


  • Organizational Affiliation
    • CAS Key Laboratory of Receptor Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit alpha-13362Homo sapiensMutation(s): 0 
Gene Names: GNA13
Membrane Entity: Yes 
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Find proteins for Q14344 (Homo sapiens)
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Go to UniProtKB:  Q14344
PHAROS:  Q14344
GTEx:  ENSG00000120063 
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UniProt GroupQ14344
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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-1371Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 35308Homo sapiensMutation(s): 0 
Gene Names: GPR35
Membrane Entity: Yes 
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Find proteins for Q9HC97 (Homo sapiens)
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PHAROS:  Q9HC97
GTEx:  ENSG00000178623 
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UniProt GroupQ9HC97
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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 
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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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth H]247Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary