8W8R

Cryo-EM structure of the AA-14-bound GPR101-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Structure of GPR101-Gs enables identification of ligands with rejuvenating potential.

Yang, Z.Wang, J.Y.Yang, F.Zhu, K.K.Wang, G.P.Guan, Y.Ning, S.L.Lu, Y.Li, Y.Zhang, C.Zheng, Y.Zhou, S.H.Wang, X.W.Wang, M.W.Xiao, P.Yi, F.Zhang, C.Zhang, P.J.Xu, F.Liu, B.H.Zhang, H.Yu, X.Gao, N.Sun, J.P.

(2024) Nat Chem Biol 20: 484-492

  • DOI: https://doi.org/10.1038/s41589-023-01456-6
  • Primary Citation of Related Structures:  
    8W8Q, 8W8R, 8W8S

  • PubMed Abstract: 

    GPR101 is an orphan G protein-coupled receptor actively participating in energy homeostasis. Here we report the cryo-electron microscopy structure of GPR101 constitutively coupled to Gs heterotrimer, which reveals unique features of GPR101, including the interaction of extracellular loop 2 within the 7TM bundle, a hydrophobic chain packing-mediated activation mechanism and the structural basis of disease-related mutants. Importantly, a side pocket is identified in GPR101 that facilitates in silico screening to identify four small-molecule agonists, including AA-14. The structure of AA-14-GPR101-Gs provides direct evidence of the AA-14 binding at the side pocket. Functionally, AA-14 partially restores the functions of GH/IGF-1 axis and exhibits several rejuvenating effects in wild-type mice, which are abrogated in Gpr101-deficient mice. In summary, we provide a structural basis for the constitutive activity of GPR101. The structure-facilitated identification of GPR101 agonists and functional analysis suggest that targeting this orphan receptor has rejuvenating potential.


  • Organizational Affiliation

    NHC Key Laboratory of Otorhinolaryngology, Qilu Hospital of Shandong University, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit362Homo sapiensMutation(s): 0 
Gene Names: GNAI1
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 
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63096P63092
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-1341Homo 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable G-protein coupled receptor 101C [auth R]508Homo sapiensMutation(s): 0 
Gene Names: GPR101
Membrane Entity: Yes 
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Find proteins for Q96P66 (Homo sapiens)
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PHAROS:  Q96P66
GTEx:  ENSG00000165370 
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UniProt GroupQ96P66
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Scfv16D [auth S]285Homo 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 Y]58Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U7D
Query on U7D

Download Ideal Coordinates CCD File 
F [auth R],
G [auth R]
1-(4-methylpyridin-2-yl)-3-[3-(trifluoromethyl)phenyl]thiourea
C14 H12 F3 N3 S
FSUJUFLZGYFLEM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31725007
National Natural Science Foundation of China (NSFC)China32130055
National Natural Science Foundation of China (NSFC)China92057121
National Science Foundation (NSF, China)China81825022
National Science Foundation (NSF, China)China82225011

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references