7YU7

Human Lysophosphatidic Acid Receptor 1-Gi complex bound to ONO-0740556, state3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Structure of the active G i -coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist.

Akasaka, H.Tanaka, T.Sano, F.K.Matsuzaki, Y.Shihoya, W.Nureki, O.

(2022) Nat Commun 13: 5417-5417

  • DOI: https://doi.org/10.1038/s41467-022-33121-2
  • Primary Citation of Related Structures:  
    7YU3, 7YU4, 7YU5, 7YU6, 7YU7, 7YU8

  • PubMed Abstract: 

    Lysophosphatidic acid receptor 1 (LPA 1 ) is one of the six G protein-coupled receptors activated by the bioactive lipid, lysophosphatidic acid (LPA). LPA 1 is a drug target for various diseases, including cancer, inflammation, and neuropathic pain. Notably, LPA 1 agonists have potential therapeutic value for obesity and urinary incontinence. Here, we report a cryo-electron microscopy structure of the active human LPA 1 -G i complex bound to ONO-0740556, an LPA analog with more potent activity against LPA 1 . Our structure elucidated the details of the agonist binding mode and receptor activation mechanism mediated by rearrangements of transmembrane segment 7 and the central hydrophobic core. A structural comparison of LPA 1 and other phylogenetically-related lipid-sensing GPCRs identified the structural determinants for lipid preference of LPA 1 . Moreover, we characterized the structural polymorphisms at the receptor-G-protein interface, which potentially reflect the G-protein dissociation process. Our study provides insights into the detailed mechanism of LPA 1 binding to agonists and paves the way toward the design of drug-like agonists targeting LPA 1 .


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lysophosphatidic acid receptor 1B [auth R]379Homo sapiensMutation(s): 0 
Gene Names: LPAR1EDG2LPA1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92633 (Homo sapiens)
Explore Q92633 
Go to UniProtKB:  Q92633
PHAROS:  Q92633
GTEx:  ENSG00000198121 
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UniProt GroupQ92633
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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]351Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
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UniProt GroupP54311
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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]68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P63212 (Bos taurus)
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UniProt GroupP63212
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth S]260Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K6L (Subject of Investigation/LOI)
Query on K6L

Download Ideal Coordinates CCD File 
F [auth R][(2~{R})-2-[5-(2-hexylphenyl)pentanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate
C20 H34 N O6 P
LYWONSBDWRVEKO-LJQANCHMSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05037

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release