8K5B

Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 (Local refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 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 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, 8K5B, 8K5C, 8K5D

  • 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

    Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human Hydroxycarboxylic acid receptor 2476Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS4 (Homo sapiens)
Explore Q8TDS4 
Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDS4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references