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 8HJ0 | pdb_00008hj0

GPR21(m5) and G15 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8HJ0

This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structures of orphan GPR21 signaling complexes.

Lin, X., Chen, B., Wu, Y., Han, Y., Qi, A., Wang, J., Yang, Z., Wei, X., Zhao, T., Wu, L., Xie, X., Sun, J., Zheng, J., Zhao, S., Xu, F.

(2023) Nat Commun 14: 216-216

  • DOI: https://doi.org/10.1038/s41467-023-35882-w
  • Primary Citation Related Structures: 
    8HIX, 8HJ0, 8HJ1, 8HJ2

  • PubMed Abstract: 

    GPR21 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for type 2 diabetes and other metabolic disorders. This receptor shows high basal activity in coupling to multiple G proteins in the absence of any known endogenous agonist or synthetic ligand. Here, we present the structures of ligand-free human GPR21 bound to heterotrimeric miniGs and miniG15 proteins, respectively. We identified an agonist-like motif in extracellular loop 2 (ECL2) that occupies the orthosteric pocket and promotes receptor activation. A side pocket that may be employed as a new ligand binding site was also uncovered. Remarkably, G protein binding is accommodated by a flexible cytoplasmic portion of transmembrane helix 6 (TM6) which adopts little or undetectable outward movement. These findings will enable the design of modulators for GPR21 for understanding its signal transduction and exploring opportunity for deorphanization.


  • Organizational Affiliation: 
    • iHuman Institute, ShanghaiTech University, Pudong, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 130.97 kDa 
  • Atom Count: 8,260 
  • Modeled Residue Count: 1,043 
  • Deposited Residue Count: 1,170 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short249Homo sapiensMutation(s): 6 
Gene Names: GNAS, GNAS1, GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]96Homo sapiensMutation(s): 1 
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
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nb35D [auth N]149Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable G-protein coupled receptor 21E [auth R]336Homo sapiensMutation(s): 0 
Gene Names: GPR21
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99679 (Homo sapiens)
Explore Q99679 
Go to UniProtKB:  Q99679
GTEx:  ENSG00000188394 
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UniProt GroupQ99679
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection