9IZG | pdb_00009izg

Cryo-EM structure of LPA1-Gq complex with LPA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 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 insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins.

Suzuki, S.Tanaka, K.Kamegawa, A.Nishikawa, K.Suzuki, H.Oshima, A.Fujiyoshi, Y.

(2024) J Struct Biol 217: 108164-108164

  • DOI: https://doi.org/10.1016/j.jsb.2024.108164
  • Primary Citation of Related Structures:  
    9IZF, 9IZG, 9IZH

  • PubMed Abstract: 

    Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are bioactive lysophospholipids derived from cell membranes that activate the endothelial differentiation gene family of G protein-coupled receptors. Activation of these receptors triggers multiple downstream signaling cascades through G proteins such as Gi/o, Gq/11, and G12/13. Therefore, LPA and S1P mediate several physiological processes, including cytoskeletal dynamics, neurite retraction, cell migration, cell proliferation, and intracellular ion fluxes. The basis for the G-protein coupling selectivity of EDG receptors, however, remains unknown. Here, we present cryo-electron microscopy structures of LPA-activated LPA1 in complexes with G i , G q , and G 13 heterotrimers . Comparison of the three LPA1-G protein structures shows clearly different conformations of intracellular loop 2 (ICL2) and ICL3 that are likely induced by the different Gα protein interfaces. Interestingly, this G-protein interface interaction is a common feature of LPA and S1P receptors. Our findings provide clues to understanding the promiscuity of G-protein coupling in the endothelial differentiation gene family.


  • Organizational Affiliation

    Advanced Research Initiative, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima Bunkyo-ku 113-8510, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]382Homo sapiensMutation(s): 0 
Gene Names: GNB1
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth C]70Mus musculusMutation(s): 0 
Gene Names: Gng2
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tagC [auth R]651Escherichia coliHomo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCLPAR1EDG2LPA1
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Find proteins for Q92633 (Homo sapiens)
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PHAROS:  Q92633
GTEx:  ENSG00000198121 
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UniProt GroupsP0ABE7Q92633
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gs-mini-Gq chimeraD [auth A]246Homo sapiensMutation(s): 0 
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Find proteins for A0A590UJY2 (Homo sapiens)
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GTEx:  ENSG00000087460 
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UniProt GroupA0A590UJY2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16E [auth S]248synthetic constructMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NKP (Subject of Investigation/LOI)
Query on NKP

Download Ideal Coordinates CCD File 
F [auth R](2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H00451

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references