9LYD | pdb_00009lyd

Cryo-EM structure of GPR3-1IU9 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 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

Structural basis of oligomerization-modulated activation and autoinhibition of orphan receptor GPR3.

Chang, H.Li, X.Tu, H.Wu, L.Yu, Y.Liu, J.Chen, N.Shen, W.L.Hua, T.

(2025) Cell Rep 44: 115478-115478

  • DOI: https://doi.org/10.1016/j.celrep.2025.115478
  • Primary Citation of Related Structures:  
    9LYB, 9LYC, 9LYD

  • PubMed Abstract: 

    G protein-coupled receptor 3 (GPR3) is a class A orphan receptor characterized by high constitutive activity in the G s signaling pathway. GPR3 has been implicated in Alzheimer's disease and the regulation of thermogenesis in human adipocytes, yet the molecular mechanisms underlying its self-activation and potential endogenous modulators remain unclear. In this study, we present cryo-electron microscopy (cryo-EM) structures of GPR3 in different oligomerization states, both in the absence and presence of G protein. Notably, in addition to the monomeric form of GPR3, our findings reveal a functional GPR3 dimer with an extensive dimer interface-a feature rarely observed in class A GPCRs. Moreover, oligomerization appears to be linked to a unique autoinhibition mechanism involving intracellular loops, which may regulate GPR3 signaling. Collectively, these results provide new insights into the oligomerization-modulated activation of orphan GPCRs, advancing our understanding of their signaling properties.


  • Organizational Affiliation
    • iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 3,Aspartate racemaseA [auth Q],
B [auth R]
485Homo sapiensMutation(s): 0 
Gene Names: GPR3ACCAPH0670
EC: 5.1.1.13
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O58403 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58403 
Go to UniProtKB:  O58403
Find proteins for P46089 (Homo sapiens)
Explore P46089 
Go to UniProtKB:  P46089
PHAROS:  P46089
GTEx:  ENSG00000181773 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP46089O58403
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32022038
National Natural Science Foundation of China (NSFC)China32230026

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references