8W8S | pdb_00008w8s

Cryo-EM structure of the AA14-bound GPR101 complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8W8S

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 57.4 kDa 
  • Atom Count: 2,265 
  • Modeled Residue Count: 281 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable G-protein coupled receptor 101A [auth R]508Homo sapiensMutation(s): 0 
Gene Names: GPR101
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P66 (Homo sapiens)
Explore Q96P66 
Go to UniProtKB:  Q96P66
PHAROS:  Q96P66
GTEx:  ENSG00000165370 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96P66
Sequence Annotations
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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
B [auth R],
C [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

View Full Validation Report



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
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary