8J6J

Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound with GSK256073


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular recognition of niacin and lipid-lowering drugs by the human hydroxycarboxylic acid receptor 2.

Zhu, S.Yuan, Q.Li, X.He, X.Shen, S.Wang, D.Li, J.Cheng, X.Duan, X.Xu, H.E.Duan, J.

(2023) Cell Rep 42: 113406-113406

  • DOI: https://doi.org/10.1016/j.celrep.2023.113406
  • Primary Citation of Related Structures:  
    8J6I, 8J6J, 8J6L

  • PubMed Abstract: 

    Niacin, an age-old lipid-lowering drug, acts through the hydroxycarboxylic acid receptor 2 (HCAR2), a G-protein-coupled receptor (GPCR). Yet, its use is hindered by side effects like skin flushing. To address this, specific HCAR2 agonists, like MK-6892 and GSK256073, with fewer adverse effects have been created. However, the activation mechanism of HCAR2 by niacin and these new agonists is not well understood. Here, we present three cryoelectron microscopy structures of Gi-coupled HCAR2 bound to niacin, MK-6892, and GSK256073. Our findings show that different ligands induce varying binding pockets in HCAR2, influenced by aromatic amino acid clusters (W91 ECL1 , H161 4.59 , W188 5.38 , H189 5.39 , and F193 5.43 ) from receptors ECL1, TM4, and TM5. Additionally, conserved residues R111 3.36 and Y284 7.43 , unique to the HCA receptor family, likely initiate activation signal propagation in HCAR2. This study provides insights into ligand recognition, receptor activation, and G protein coupling mediated by HCAR2, laying the groundwork for developing HCAR2-targeted drugs.


  • Organizational Affiliation

    School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacology, Guilin Medical University, Guilin 541004, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1370Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
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]70Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Scfv16D [auth H]247Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxycarboxylic acid receptor 2,hydroxycarboxylic acid receptor 2E [auth R]488Homo sapiensMutation(s): 0 
Gene Names: HCAR2GPR109AHCA2HM74ANIACR1
Membrane Entity: Yes 
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Find proteins for Q8TDS4 (Homo sapiens)
Explore Q8TDS4 
Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
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UniProt GroupQ8TDS4
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OKL
Query on OKL

Download Ideal Coordinates CCD File 
F [auth R]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: 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
National Natural Science Foundation of China (NSFC)China--
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release