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- EMDB-63717: GPR3 dimer with antagonist AF64394 -

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Basic information

Entry
Database: EMDB / ID: EMD-63717
TitleGPR3 dimer with antagonist AF64394
Map data
Sample
  • Complex: GPR3 dimer with antagonist AF64394
    • Protein or peptide: Soluble cytochrome b562,G-protein coupled receptor 3
  • Ligand: (Z)-N-(2-hydroxyethyl)octadec-9-enamide
  • Ligand: 1-DODECANOL
  • Ligand: (4Z)-oct-4-en-1-ol
  • Ligand: N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
KeywordsGPCR / dimer / antagonist / MEMBRANE PROTEIN
Function / homology
Function and homology information


sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / regulation of metabolic process / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / periplasmic space / electron transfer activity / iron ion binding ...sphingosine-1-phosphate receptor activity / regulation of meiotic nuclear division / regulation of metabolic process / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane / cytoplasm
Similarity search - Function
G protein-coupled receptor 3 / G protein-coupled receptor 3/6/12 orphan / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / G-protein coupled receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsGeng C / Jun X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism and function of GPR3 regulated by a negative allosteric modulator.
Authors: Geng Chen / Jana Bláhová / Nico Staffen / Harald Hübner / Nadja Nunhöfer / Chen Qiu / Peter Gmeiner / Dorothee Weikert / Yang Du / Jun Xu /
Abstract: Allosteric modulators have gained substantial interest in current GPCR drug discovery. Here, we present a mechanism of allosteric modulation involving the dimerization of GPR3, a promising drug ...Allosteric modulators have gained substantial interest in current GPCR drug discovery. Here, we present a mechanism of allosteric modulation involving the dimerization of GPR3, a promising drug target for metabolic diseases and central nervous system disorders. We show that GPR3 forms constitutive homodimers in live cells and reveal that the inhibitor AF64394 functions as a negative allosteric modulator (NAM) specifically targeting dimeric GPR3. Using cryogenic electron microscopy (cryo-EM), we determine the structures of the AF64394-bound GPR3 dimer and its dimer-Gs signaling complex. These high-resolution structures reveal that AF64394 binds to the transmembrane dimer interface. AF64394 binding prevents the dissociation of the GPR3 dimer upon engagement with Gs and restrains transmembrane helix 5 in an inactive-like intermediate conformation, leading to reduced coupling with Gs. Our studies unveil a mechanism of dimer-specific inhibition of signaling with significant implications for the discovery of drugs targeting GPCRs capable of dimerization.
History
DepositionMar 12, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63717.png

Downloads & links

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Map

FileDownload / File: emd_63717.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0320507 - 1.345961
Average (Standard dev.)-0.0003189499 (±0.021672403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfA map

Fileemd_63717_half_map_1.map
AnnotationhalfA_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB map

Fileemd_63717_half_map_2.map
AnnotationhalfB map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPR3 dimer with antagonist AF64394

EntireName: GPR3 dimer with antagonist AF64394
Components
  • Complex: GPR3 dimer with antagonist AF64394
    • Protein or peptide: Soluble cytochrome b562,G-protein coupled receptor 3
  • Ligand: (Z)-N-(2-hydroxyethyl)octadec-9-enamide
  • Ligand: 1-DODECANOL
  • Ligand: (4Z)-oct-4-en-1-ol
  • Ligand: N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine

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Supramolecule #1: GPR3 dimer with antagonist AF64394

SupramoleculeName: GPR3 dimer with antagonist AF64394 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Soluble cytochrome b562,G-protein coupled receptor 3

MacromoleculeName: Soluble cytochrome b562,G-protein coupled receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.446375 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: DYKDDDDKLE VLFQGPGSAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLMMWGA GSPLAWLSAG SGNVNVSSVG PAEGPTGPAA P LPSPKAWD ...String:
DYKDDDDKLE VLFQGPGSAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLMMWGA GSPLAWLSAG SGNVNVSSVG PAEGPTGPAA P LPSPKAWD VVLCISGTLV SCENALVVAI IVGTPAFRAP MFLLVGSLAV ADLLAGLGLV LHFAAVFCIG SAEMSLVLVG VL AMAFTAS IGSLLAITVD RYLSLYNALT YYSETTVTRT YVMLALVWGG ALGLGLLPVL AWNCLDGLTT CGVVYPLSKN HLV VLAIAF FMVFGIMLQL YAQICRIVCR HAQQIALQRH LLPASHYVAT RKGIATLAVV LGAFAACWLP FTVYCLLGDA HSPP LYTYL TLLPATYNSM INPIIYAFRN QDVQKVLWAV CCCCSSSKIP FRSRSPSDVL EHHHHHHHHH H

UniProtKB: Soluble cytochrome b562, G-protein coupled receptor 3

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Macromolecule #2: (Z)-N-(2-hydroxyethyl)octadec-9-enamide

MacromoleculeName: (Z)-N-(2-hydroxyethyl)octadec-9-enamide / type: ligand / ID: 2 / Number of copies: 2 / Formula: 5YM
Molecular weightTheoretical: 325.529 Da
Chemical component information

ChemComp-5YM:
(Z)-N-(2-hydroxyethyl)octadec-9-enamide

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Macromolecule #3: 1-DODECANOL

MacromoleculeName: 1-DODECANOL / type: ligand / ID: 3 / Number of copies: 4 / Formula: 1DO
Molecular weightTheoretical: 186.334 Da
Chemical component information

ChemComp-1DO:
1-DODECANOL

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Macromolecule #4: (4Z)-oct-4-en-1-ol

MacromoleculeName: (4Z)-oct-4-en-1-ol / type: ligand / ID: 4 / Number of copies: 4 / Formula: A1AJD
Molecular weightTheoretical: 128.212 Da

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Macromolecule #5: N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]t...

MacromoleculeName: N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine
type: ligand / ID: 5 / Number of copies: 2 / Formula: A1EM2
Molecular weightTheoretical: 393.869 Da

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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 / Details: 20mM NaCl, 100mM Hepes, 0.003% LMNG, 0.001% GDN
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8x2k

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98600
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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