8I7W

Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 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

Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2.

Park, J.H.Kawakami, K.Ishimoto, N.Ikuta, T.Ohki, M.Ekimoto, T.Ikeguchi, M.Lee, D.S.Lee, Y.H.Tame, J.R.H.Inoue, A.Park, S.Y.

(2023) Nat Commun 14: 7150-7150

  • DOI: https://doi.org/10.1038/s41467-023-42764-8
  • Primary Citation of Related Structures:  
    8I7V, 8I7W

  • PubMed Abstract: 

    Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce G i/o signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with lipolytic and atherogenic activity, and neuroinflammation. Although many reports have elucidated the function of HCAR2 and its potential as a therapeutic target for treating not only dyslipidemia but also neuroimmune disorders such as multiple sclerosis and Parkinson's disease, the structural basis of ligand recognition and ligand-induced G i -coupling remains unclear. Here we report three cryo-EM structures of the human HCAR2-G i signaling complex, each bound with different ligands: niacin, acipimox or GSK256073. All three agonists are held in a deep pocket lined by residues that are not conserved in HCAR1 and HCAR3. A distinct hairpin loop at the HCAR2 N-terminus and extra-cellular loop 2 (ECL2) completely enclose the ligand. These structures also reveal the agonist-induced conformational changes propagated to the G-protein-coupling interface during activation. Collectively, the structures presented here are expected to help in the design of ligands specific for HCAR2, leading to new drugs for the treatment of various diseases such as dyslipidemia and inflammation.


  • Organizational Affiliation

    Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk, 28119, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human hydroxycarboxylic acid receptor 2,Hydroxycarboxylic acid receptor 2476Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS4 (Homo sapiens)
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Go to UniProtKB:  Q8TDS4
GTEx:  ENSG00000182782 
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UniProt GroupQ8TDS4
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
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Find proteins for P63096 (Homo sapiens)
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GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-280Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16257Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OKL (Subject of Investigation/LOI)
Query on OKL

Download Ideal Coordinates CCD File 
F [auth A]8-chloranyl-3-pentyl-7H-purine-2,6-dione
C10 H13 Cl N4 O2
CGAMDQCXAAOFSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

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: 2024-02-07
    Type: Initial release