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- PDB-9lyd: Cryo-EM structure of GPR3-1IU9 complex -

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Basic information

Entry
Database: PDB / ID: 9lyd
TitleCryo-EM structure of GPR3-1IU9 complex
ComponentsG-protein coupled receptor 3,Aspartate racemase
KeywordsSTRUCTURAL PROTEIN / GPCR / G protein / cryo-EM / membrane protein
Function / homology
Function and homology information


aspartate racemase activity / aspartate racemase / sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / regulation of metabolic process / positive regulation of cAMP/PKA signal transduction / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis ...aspartate racemase activity / aspartate racemase / sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / regulation of metabolic process / positive regulation of cAMP/PKA signal transduction / regulation of cytosolic calcium ion concentration / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / plasma membrane / cytoplasm
Similarity search - Function
G protein-coupled receptor 3 / Aspartate racemase / G protein-coupled receptor 3/6/12 orphan / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Aspartate and glutamate racemases signature 2. / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / G-protein coupled receptors family 1 signature. ...G protein-coupled receptor 3 / Aspartate racemase / G protein-coupled receptor 3/6/12 orphan / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Aspartate and glutamate racemases signature 2. / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Aspartate racemase / G-protein coupled receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsHua, T. / Liu, Z.J. / Li, X.T. / Chang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32022038 China
National Natural Science Foundation of China (NSFC)32230026 China
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of oligomerization-modulated activation and autoinhibition of orphan receptor GPR3.
Authors: Hao Chang / Xiaoting Li / Hongqing Tu / Lijie Wu / Yanan Yu / Junlin Liu / Na Chen / Wei L Shen / Tian Hua /
Abstract: G protein-coupled receptor 3 (GPR3) is a class A orphan receptor characterized by high constitutive activity in the G signaling pathway. GPR3 has been implicated in Alzheimer's disease and the ...G protein-coupled receptor 3 (GPR3) is a class A orphan receptor characterized by high constitutive activity in the G 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.
History
DepositionFeb 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
Q: G-protein coupled receptor 3,Aspartate racemase
R: G-protein coupled receptor 3,Aspartate racemase


Theoretical massNumber of molelcules
Total (without water)104,8192
Polymers104,8192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein G-protein coupled receptor 3,Aspartate racemase / ACCA orphan receptor


Mass: 52409.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR3, ACCA, PH0670 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P46089, UniProt: O58403, aspartate racemase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: dimer state of GPR3 with PGS / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205789 / Symmetry type: POINT
Atomic model buildingB value: 118.6 / Protocol: RIGID BODY FIT

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