9D0A | pdb_00009d0a

CryoEM structure of PAR2 with endogenous tethered ligand.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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(T) subunit beta-1A [auth B]339Homo sapiensMutation(s): 0 
Gene Names: GNB1
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth G]59Homo sapiensMutation(s): 0 
Gene Names: GNG2
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth E]251unidentifiedMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase-activated receptor 2D [auth R]397Homo sapiensMutation(s): 0 
Gene Names: F2RL1GPR11PAR2
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GTEx:  ENSG00000164251 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(q) subunit alpha, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short chimera,Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortE [auth A]360Homo sapiensMutation(s): 0 
Gene Names: GNAQGAQGNASGNAS1GSP
EC: 3.6.5
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Find proteins for P63092 (Homo sapiens)
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PHAROS:  P63092
GTEx:  ENSG00000087460 
Find proteins for P50148 (Homo sapiens)
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PHAROS:  P50148
GTEx:  ENSG00000156052 
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UniProt GroupsP63092P50148
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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