8JIM | pdb_00008jim

Cryo-EM structure of MMF bound ketone body receptor HCAR2-Gi signaling complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Biased allosteric activation of ketone body receptor HCAR2 suppresses inflammation.

Zhao, C.Wang, H.Liu, Y.Cheng, L.Wang, B.Tian, X.Fu, H.Wu, C.Li, Z.Shen, C.Yu, J.Yang, S.Hu, H.Fu, P.Ma, L.Wang, C.Yan, W.Shao, Z.

(2023) Mol Cell 83: 3171

  • DOI: https://doi.org/10.1016/j.molcel.2023.07.030
  • Primary Citation Related Structures: 
    8JHY, 8JII, 8JIL, 8JIM

  • PubMed Abstract: 

    Hydroxycarboxylic acid receptor 2 (HCAR2), modulated by endogenous ketone body β-hydroxybutyrate and exogenous niacin, is a promising therapeutic target for inflammation-related diseases. HCAR2 mediates distinct pathophysiological events by activating G i/o protein or β-arrestin effectors. Here, we characterize compound 9n as a G i -biased allosteric modulator (BAM) of HCAR2 and exhibit anti-inflammatory efficacy in RAW264.7 macrophages via a specific HCAR2-G i pathway. Furthermore, four structures of HCAR2-G i complex bound to orthosteric agonists (niacin or monomethyl fumarate), compound 9n, and niacin together with compound 9n simultaneously reveal a common orthosteric site and a unique allosteric site. Combined with functional studies, we decipher the action framework of biased allosteric modulation of compound 9n on the orthosteric site. Moreover, co-administration of compound 9n with orthosteric agonists could enhance anti-inflammatory effects in the mouse model of colitis. Together, our study provides insight to understand the molecular pharmacology of the BAM and facilitates exploring the therapeutic potential of the BAM with orthosteric drugs.


  • Organizational Affiliation
    • Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, Sichuan, China.

Macromolecule Content 

  • Total Structure Weight: 162.6 kDa 
  • Atom Count: 9,051 
  • Modeled Residue Count: 1,144 
  • Deposited Residue Count: 1,444 
  • Unique protein chains: 5

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]356Homo 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 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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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]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1C [auth D]354Homo sapiensMutation(s): 4 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
Explore P63096 
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv16D [auth S]266Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Hydroxycarboxylic acid receptor 2397Homo sapiensMutation(s): 0 
Gene Names: HCAR2GPR109AHCA2HM74ANIACR1
Membrane Entity: Yes 
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Find proteins for Q8TDS4 (Homo sapiens)
Explore Q8TDS4 
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PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
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UniProt GroupQ8TDS4
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 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--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary