7XK2

Cryo-EM Structure of Human Niacin Receptor HCA2-Gi protein complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the human niacin receptor HCA2-G i signalling complex.

Yang, Y.Kang, H.J.Gao, R.Wang, J.Han, G.W.DiBerto, J.F.Wu, L.Tong, J.Qu, L.Wu, Y.Pileski, R.Li, X.Zhang, X.C.Zhao, S.Kenakin, T.Wang, Q.Stevens, R.C.Peng, W.Roth, B.L.Rao, Z.Liu, Z.J.

(2023) Nat Commun 14: 1692-1692

  • DOI: https://doi.org/10.1038/s41467-023-37177-6
  • Primary Citation of Related Structures:  
    7XK2, 7ZL9, 7ZLY

  • PubMed Abstract: 

    The hydroxycarboxylic acid receptor 2 (HCA2) agonist niacin has been used as treatment for dyslipidemia for several decades albeit with skin flushing as a common side-effect in treated individuals. Extensive efforts have been made to identify HCA2 targeting lipid lowering agents with fewer adverse effects, despite little being known about the molecular basis of HCA2 mediated signalling. Here, we report the cryo-electron microscopy structure of the HCA2-G i signalling complex with the potent agonist MK-6892, along with crystal structures of HCA2 in inactive state. These structures, together with comprehensive pharmacological analysis, reveal the ligand binding mode and activation and signalling mechanisms of HCA2. This study elucidates the structural determinants essential for HCA2 mediated signalling and provides insights into ligand discovery for HCA2 and related receptors.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1356Homo sapiensMutation(s): 0 
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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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
Sequence Annotations
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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(T) subunit beta-1340Homo 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
Hydroxycarboxylic acid receptor 2C [auth R]325Homo sapiensMutation(s): 0 
Gene Names: HCAR2
Membrane Entity: Yes 
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Find proteins for Q8TDS4 (Homo sapiens)
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Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
GTEx:  ENSG00000182782 
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UniProt GroupQ8TDS4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth S]248Homo sapiensMutation(s): 0 
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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]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
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 R]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:  7XK2 Ki: min: 4, max: 595 (nM) from 2 assay(s)
EC50: min: 16, max: 4600 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2017YFC0840300
Chinese Academy of SciencesChinaXDB08020200
National Natural Science Foundation of China (NSFC)China31330019
Ministry of Science and Technology (MoST, China)China2014CB910400 and 2015CB910104
National Science Foundation (NSF, China)China2016YCF0905902

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-12-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary