8IHJ

Cryo-EM structure of HCA3-Gi complex with acifran


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding.

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

(2023) Nat Commun 14: 5899-5899

  • DOI: https://doi.org/10.1038/s41467-023-41650-7
  • Primary Citation of Related Structures:  
    8IHB, 8IHF, 8IHH, 8IHI, 8IHJ, 8IHK

  • PubMed Abstract: 

    Hydroxycarboxylic acid receptors (HCA) are expressed in various tissues and immune cells. HCA2 and its agonist are thus important targets for treating inflammatory and metabolic disorders. Only limited information is available, however, on the active-state binding of HCAs with agonists. Here, we present cryo-EM structures of human HCA2-Gi and HCA3-Gi signaling complexes binding with multiple compounds bound. Agonists were revealed to form a salt bridge with arginine, which is conserved in the HCA family, to activate these receptors. Extracellular regions of the receptors form a lid-like structure that covers the ligand-binding pocket. Although transmembrane (TM) 6 in HCAs undergoes dynamic conformational changes, ligands do not directly interact with amino acids in TM6, suggesting that indirect signaling induces a slight shift in TM6 to activate Gi proteins. Structural analyses of agonist-bound HCA2 and HCA3 together with mutagenesis and molecular dynamics simulation provide molecular insights into HCA ligand recognition and activation mechanisms.


  • Organizational Affiliation

    TMDU Advanced Research Institute, Tokyo Medical and Dental University Bunkyo-ku, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Hydroxycarboxylic acid receptor 3A [auth R]530Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 2 
Gene Names: cybCHCAR3GPR109BHCA3HM74BNIACR2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P49019 (Homo sapiens)
Explore P49019 
Go to UniProtKB:  P49019
PHAROS:  P49019
GTEx:  ENSG00000255398 
Entity Groups  
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UniProt GroupsP0ABE7P49019
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 2 
Gene Names: GNAI1
EC: 3.6.5
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth S]248synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]382Mus musculusMutation(s): 0 
Gene Names: Gnb1
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Find proteins for P62874 (Mus musculus)
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Go to UniProtKB:  P62874
IMPC:  MGI:95781
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth C]70Mus musculusMutation(s): 0 
Gene Names: Gng2
Membrane Entity: Yes 
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Find proteins for P63213 (Mus musculus)
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Go to UniProtKB:  P63213
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UniProt GroupP63213
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P9X (Subject of Investigation/LOI)
Query on P9X

Download Ideal Coordinates CCD File 
F [auth R](5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid
C12 H10 O4
DFDGRKNOFOJBAJ-LBPRGKRZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P9X BindingDB:  8IHJ IC50: min: 500, max: 3000 (nM) from 2 assay(s)
EC50: min: 160, max: 4200 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 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)Japan20H00451

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary