9E7R | pdb_00009e7r

CryoEM structure of PAR2 with GB88


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for the activation of proteinase-activated receptors PAR1 and PAR2.

Lyu, Z.Lyu, X.Malyutin, A.G.Xia, G.Carney, D.Alves, V.M.Falk, M.Arora, N.Zou, H.McGrath, A.P.Kang, Y.

(2025) Nat Commun 16: 3931-3931

  • DOI: https://doi.org/10.1038/s41467-025-59138-x
  • Primary Citation of Related Structures:  
    9D0A, 9D4Z, 9E7R

  • PubMed Abstract: 

    Members of the proteinase-activated receptor (PAR) subfamily of G protein-coupled receptors (GPCRs) play critical roles in processes like hemostasis, thrombosis, development, wound healing, inflammation, and cancer progression. Comprising PAR1-PAR4, these receptors are specifically activated by protease cleavage at their extracellular amino terminus, revealing a 'tethered ligand' that self-activates the receptor. This triggers complex intracellular signaling via G proteins and beta-arrestins, linking external protease signals to cellular functions. To date, direct structural visualization of these ligand-receptor complexes has been limited. Here, we present structural snapshots of activated PAR1 and PAR2 bound to their endogenous tethered ligands, revealing a shallow and constricted orthosteric binding pocket. Comparisons with antagonist-bound structures show minimal conformational changes in the TM6 helix and larger movements of TM7 upon activation. These findings reveal a common activation mechanism for PAR1 and PAR2, highlighting critical residues involved in ligand recognition. Additionally, the structure of PAR2 bound to a pathway selective antagonist, GB88, demonstrates how potent orthosteric engagement can be achieved by a small molecule mimicking the endogenous tethered ligand's interactions.


  • Organizational Affiliation

    Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2A [auth G]59Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase-activated receptor 2B [auth R]337Homo sapiensMutation(s): 0 
Gene Names: F2RL1GPR11PAR2
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Find proteins for P55085 (Homo sapiens)
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Go to UniProtKB:  P55085
PHAROS:  P55085
GTEx:  ENSG00000164251 
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UniProt GroupP55085
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha chimeraC [auth A]360Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]339Homo sapiensMutation(s): 0 
Gene Names: GNB1
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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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16251Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BF3 (Subject of Investigation/LOI)
Query on A1BF3

Download Ideal Coordinates CCD File 
F [auth R]N-[(2S)-3-cyclohexyl-1-{[(2S,3S)-3-methyl-1-oxo-1-(spiro[indene-1,4'-piperidin]-1'-yl)pentan-2-yl]amino}-1-oxopropan-2-yl]-1,2-oxazole-5-carboxamide
C32 H42 N4 O4
DCUDDCGUKZLQLN-MCOVPRHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2025-05-07
    Type: Initial release