9WXM | pdb_00009wxm

Cryo-EM structure of the full-length GPR15L bound GPR15-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular insights into ligand recognition and receptor activation of GPR15.

Chen, S.Han, X.Zhang, Y.Ma, L.Yi, C.Chu, X.Tan, Q.Han, S.Zhao, Q.Wu, B.

(2025) iScience 28: 113935-113935

  • DOI: https://doi.org/10.1016/j.isci.2025.113935
  • Primary Citation of Related Structures:  
    9WXM

  • PubMed Abstract: 

    In response to the chemokine-like peptide GPR15L, G protein-coupled receptor 15 (GPR15) is crucial for immune cell trafficking and inflammatory diseases. However, understanding of its physiology and pathology is hindered by lack of molecular details of the interaction between GPR15 and the full-length GPR15L. Here, we report the structure of GPR15 bound to the full-length GPR15L and G i3 protein. Combined with mutagenesis data, this structure reveals key interactions that define ligand recognition and a subpocket that governs GPR15L selectivity and receptor activation. Molecular dynamics simulations suggest that sulfation modifications in the N-terminal region of GPR15 may play a role in stabilizing the binding between GPR15 and the core region of GPR15L. Furthermore, molecular docking of some potential small-molecule antagonists suggests a conserved molecular pattern of these ligands inhibiting receptor activation. These findings provide essential insight into functional modulation of GPR15 and would facilitate development of therapeutic strategies for treatment of inflammation and immune diseases.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein GPR15LGA [auth L]58Homo sapiensMutation(s): 0 
Gene Names: GPR15LGC10orf99GPR15LUNQ1833/PRO3446
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PHAROS:  Q6UWK7
GTEx:  ENSG00000188373 
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UniProt GroupQ6UWK7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 15B [auth R]379Homo sapiensMutation(s): 0 
Gene Names: GPR15
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PHAROS:  P49685
GTEx:  ENSG00000154165 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-3C [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI3
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GTEx:  ENSG00000065135 
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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]351Homo sapiensMutation(s): 0 
Gene Names: GNB1
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GTEx:  ENSG00000078369 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth C]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
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GTEx:  ENSG00000186469 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16F [auth D]267Mus musculusMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China82121005

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references