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- EMDB-63522: Cryo-EM structure of GPR3-1IU9 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63522
TitleCryo-EM structure of GPR3-1IU9 complex
Map data
Sample
  • Complex: dimer state of GPR3-1IU9
KeywordsGPCR / G protein / cryo-EM / membrane protein / STRUCTURAL 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsHua T / Liu ZJ / Li XT / Chang H
Funding support China, 2 items
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 21, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63522.png

Downloads & links

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Map

FileDownload / File: emd_63522.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.001644624 - 1.8990179
Average (Standard dev.)0.0018222984 (±0.02763449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63522_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63522_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimer state of GPR3-1IU9

EntireName: dimer state of GPR3-1IU9
Components
  • Complex: dimer state of GPR3-1IU9

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Supramolecule #1: dimer state of GPR3-1IU9

SupramoleculeName: dimer state of GPR3-1IU9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1iu9


Details: GPR3:AlphaFOLD2 PGS:1IU9
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

1iu9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Overall B value: 118.6
Output model

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

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