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- EMDB-51286: Cryo-EM GPCR focused map of the GPR55-G13-complex bound to lysoph... -

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Basic information

Entry
Database: EMDB / ID: EMD-51286
TitleCryo-EM GPCR focused map of the GPR55-G13-complex bound to lysophosphatidylinositol.
Map data
Sample
  • Complex: GPR55 in complex with heterotrimeric G13 protein and endogenous lipid agonist lysophosphatidylinositol
KeywordsG protein-coupled receptor / GPCR / lipid agonist / cholesterol / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsClaff T / Ebenhoch R / Weichert D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for lipid-mediated activation of G protein-coupled receptor GPR55.
Authors: Tobias Claff / Rebecca Ebenhoch / Jörg T Kley / Aniket Magarkar / Herbert Nar / Dietmar Weichert /
Abstract: GPR55 is an orphan G protein-coupled receptor (GPCR) and represents a promising drug target for cancer, inflammation, and metabolic diseases. The endogenous activation of lipid GPCRs can be solely ...GPR55 is an orphan G protein-coupled receptor (GPCR) and represents a promising drug target for cancer, inflammation, and metabolic diseases. The endogenous activation of lipid GPCRs can be solely mediated by membrane components and different lipids have been proposed as endogenous activators of GPR55, such as cannabinoids and lysophosphatidylinositols. Here, we determine high-resolution cryo-electron microscopy structures of the activated GPR55 in complex with heterotrimeric G and two structurally diverse ligands: the putative endogenous agonist 1-palmitoyl-2-lysophosphatidylinositol (LPI) and the synthetic agonist ML184. These results reveal insights into ligand recognition at GPR55, G protein coupling and receptor activation. Notably, an orthosteric binding site opening towards the membrane is observed in both structures, enabling direct interaction of the agonists with membrane lipids. The structural observations are supported by mutagenesis and functional experiments employing G protein dissociation assays. These findings will be of importance for the structure-based development of drugs targeting GPR55.
History
DepositionAug 6, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51286.png

Downloads & links

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Map

FileDownload / File: emd_51286.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285.3 Å		0.95 Å/pix.
x 300 pix.
= 285.3 Å		0.95 Å/pix.
x 300 pix.
= 285.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.951 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.556
Minimum - Maximum-3.8056448 - 4.8075647
Average (Standard dev.)-0.0009231145 (±0.043003466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51286_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: #2

Fileemd_51286_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 : GPR55 in complex with heterotrimeric G13 protein and endogenous l...

EntireName: GPR55 in complex with heterotrimeric G13 protein and endogenous lipid agonist lysophosphatidylinositol
Components
  • Complex: GPR55 in complex with heterotrimeric G13 protein and endogenous lipid agonist lysophosphatidylinositol

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Supramolecule #1: GPR55 in complex with heterotrimeric G13 protein and endogenous l...

SupramoleculeName: GPR55 in complex with heterotrimeric G13 protein and endogenous lipid agonist lysophosphatidylinositol
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15173387
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 397853
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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