7XZ6

GPR119-Gs-APD668 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Structural identification of lysophosphatidylcholines as activating ligands for orphan receptor GPR119.

Xu, P.Huang, S.Guo, S.Yun, Y.Cheng, X.He, X.Cai, P.Lan, Y.Zhou, H.Jiang, H.Jiang, Y.Xie, X.Xu, H.E.

(2022) Nat Struct Mol Biol 29: 863-870

  • DOI: https://doi.org/10.1038/s41594-022-00816-5
  • Primary Citation of Related Structures:  
    7XZ5, 7XZ6

  • PubMed Abstract: 

    Lysophosphatidylcholine (LPC) is an essential mediator in human lipid metabolism and is associated with a variety of diseases, but the exact identity of LPC receptors remains controversial. Through extensive biochemical and structural analyses, we have identified the orphan receptor GPR119 as the receptor for LPC. The structure of the GPR119-G-protein complex without any added ligands reveals a density map that fits well with LPC, which is further confirmed by mass spectrometry and functional studies. As LPCs are abundant on the cell membrane, their preoccupancy in the receptor may lead to 'constitutive activity' of GPR119. The structure of GPR119 bound to APD668, a clinical drug candidate for type 2 diabetes, reveals an exceedingly similar binding mode to LPC. Together, these data highlight structural evidence for LPC function in regulating glucose-dependent insulin secretion through direct binding and activation of GPR119, and provide structural templates for drug design targeting GPR119.


  • Organizational Affiliation

    The CAS Key Laboratory of Receptor Research, 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 G(s) subunit alpha isoforms short394Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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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-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody35D [auth N]139Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Glucose-dependent insulinotropic receptorE [auth R]485Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCGPR119
Membrane Entity: Yes 
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Find proteins for Q8TDV5 (Homo sapiens)
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PHAROS:  Q8TDV5
GTEx:  ENSG00000147262 
Find proteins for P0ABE7 (Escherichia coli)
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UniProt GroupsQ8TDV5P0ABE7
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I7J (Subject of Investigation/LOI)
Query on I7J

Download Ideal Coordinates CCD File 
F [auth R]propan-2-yl 4-[1-(2-fluoranyl-4-methylsulfonyl-phenyl)pyrazolo[3,4-d]pyrimidin-4-yl]oxypiperidine-1-carboxylate
C21 H24 F N5 O5 S
XTRUQJBVQBUKSQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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)China2018YFA0507002

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references