8IYH

Structure of MK6892-GPR109A-G-protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution.

Yadav, M.K.Sarma, P.Maharana, J.Ganguly, M.Mishra, S.Zaidi, N.Dalal, A.Singh, V.Saha, S.Mahajan, G.Sharma, S.Chami, M.Banerjee, R.Shukla, A.K.

(2024) Nat Commun 15: 1939-1939

  • DOI: https://doi.org/10.1038/s41467-024-46239-2
  • Primary Citation of Related Structures:  
    8IY9, 8IYH, 8IYW, 8JER, 8JHN

  • PubMed Abstract: 

    The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical GPCR that plays a central role in the inhibition of lipolytic and atherogenic activities. Its activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. GPR109A continues to be a target for developing potential therapeutics in dyslipidemia with minimized flushing response. Here, we present cryo-EM structures of the GPR109A in complex with dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures elucidate the binding mechanism of agonists, molecular basis of receptor activation, and insights into biased signaling elicited by some of the agonists. The structural framework also allows us to engineer receptor mutants that exhibit G-protein signaling bias, and therefore, our study may help in structure-guided drug discovery efforts targeting this receptor.


  • Organizational Affiliation

    Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1350Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(o) subunit alpha240Homo sapiensMutation(s): 6 
Gene Names: GNAO1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P09471 (Homo sapiens)
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Go to UniProtKB:  P09471
PHAROS:  P09471
GTEx:  ENSG00000087258 
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UniProt GroupP09471
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxycarboxylic acid receptor 2C [auth D]419Homo sapiensMutation(s): 0 
Gene Names: CHRM4HCAR2
Membrane Entity: Yes 
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Find proteins for P08173 (Homo sapiens)
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Go to UniProtKB:  P08173
PHAROS:  P08173
GTEx:  ENSG00000180720 
Find proteins for Q8TDS4 (Homo sapiens)
Explore Q8TDS4 
Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
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UniProt GroupsP08173Q8TDS4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ScFv16 AntibodyE [auth H]248Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FI7 (Subject of Investigation/LOI)
Query on FI7

Download Ideal Coordinates CCD File 
F [auth D]2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid
C19 H22 N4 O5
CJHXBFSJXDUJHP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FI7 BindingDB:  8IYH Ki: min: 4, max: 595 (nM) from 2 assay(s)
EC50: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR29041/BRB/10/1697/20

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary