9GE2 | pdb_00009ge2

Structure of GPR55 in complex with G13 and synthetic agonist ML184


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for lipid-mediated activation of G protein-coupled receptor GPR55.

Claff, T.Ebenhoch, R.Kley, J.T.Magarkar, A.Nar, H.Weichert, D.

(2025) Nat Commun 16: 1973-1973

  • DOI: https://doi.org/10.1038/s41467-025-57204-y
  • Primary Citation of Related Structures:  
    9GE2, 9GE3

  • PubMed 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 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 13 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.


  • Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Global Medicinal Chemistry, Biberach an der Riß, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit alpha-13230Homo sapiensMutation(s): 7 
Gene Names: GNA13
UniProt & NIH Common Fund Data Resources
Find proteins for Q14344 (Homo sapiens)
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Go to UniProtKB:  Q14344
PHAROS:  Q14344
GTEx:  ENSG00000120063 
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UniProt GroupQ14344
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1358Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Single-chain variable fragment ScFv16C [auth F]253Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]80Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,G-protein coupled receptor 55E [auth R]650Aequorea victoriaHomo sapiens
This entity is chimeric
Mutation(s): 6 
Gene Names: GFPGPR55
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Find proteins for Q9Y2T6 (Homo sapiens)
Explore Q9Y2T6 
Go to UniProtKB:  Q9Y2T6
PHAROS:  Q9Y2T6
GTEx:  ENSG00000135898 
Entity Groups  
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UniProt GroupQ9Y2T6
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9Y2T6-1
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth X]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IKH (Subject of Investigation/LOI)
Query on A1IKH

Download Ideal Coordinates CCD File 
G [auth R]3-[4-(2,3-dimethylphenyl)piperazin-1-yl]carbonyl-N,N-dimethyl-4-pyrrolidin-1-yl-benzenesulfonamide
C25 H34 N4 O3 S
VRSJAHQGJHDACS-UHFFFAOYSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
H [auth R]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release