8YYX | pdb_00008yyx

Cryo-EM structure of OXGR1 bound to leukotriene E4 and Gq proteins


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Molecular insights into ligand recognition and signaling of OXGR1.

Liu, A.Liu, Y.Long, Y.Ye, R.D.

(2025) Nat Commun 16: 11205-11205

  • DOI: https://doi.org/10.1038/s41467-025-67101-z
  • Primary Citation Related Structures: 
    8YYW, 8YYX

  • PubMed Abstract: 

    GPR99/OXGR1 is a G protein-coupled receptor (GPCR) with two endogenous agonists, the tricarboxylic acid cycle derivative 2-oxoglutarate (α-ketoglutarate) and the inflammatory mediator cysteinyl leukotriene E4 (LTE 4 ), hence also termed CysLT3 receptor. How GPR99/OXGR1 recognizes two distinct ligands is a biologically important question. Here we present cryo-EM structures of GPR99/OXGR1-Gq complexed with oxoglutarate and LTE 4 , respectively. The oxoglutarate-bound structure shows a binding pocket surrounded by the transmembrane domains (TM), with a primary site and an accessory site for simultaneous binding of two oxoglutarate molecules for full activation of the receptor. The TM binding pocket, however, is too small to accommodate the cysteinyl leukotriene LTE 4 . Alanine substitution of key residues for oxoglutarate binding had little impact on LTE 4 -induced signaling. A distinct site in between TM3/4/5 just above intracellular loop 2 was identified in the solved structure with LTE 4 , but the densities were less well-defined. Alanine substitution of amino acids potentially involved in LTE 4 interaction at this site abrogated LTE 4 -induced receptor activation without affecting oxoglutarate-induced signaling. Both ligands activated GPR99/OXGR1 primarily through the Gq pathway, but LTE 4 also induced Gi signaling. These findings illustrate the structural basis for GPR99/OXGR1 to interact with structurally distict oxoglutarate and LTE 4 .


  • Organizational Affiliation
    • The Affiliated Dongguan Songshan Lake Central Hospital, Guangdong Medical University, Dongguan, Guangdong, China. liuaijun@cuhk.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 151.15 kDa 
  • Atom Count: 9,103 
  • Modeled Residue Count: 1,152 
  • Deposited Residue Count: 1,348 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
scFV16247Vicugna pacosMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1339Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
Entity Groups
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UniProt GroupP62873
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha354Homo sapiensMutation(s): 2 
Gene Names: GNAI1GNAQGAQ
EC: 3.6.5
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
2-oxoglutarate receptor 1337Homo sapiensMutation(s): 0 
Gene Names: OXGR1GPR80GPR99P2RY15P2Y15
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PHAROS:  Q96P68
GTEx:  ENSG00000165621 
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D7P
(Subject of Investigation/LOI)

Query on A1D7P



Download:Ideal Coordinates CCD File
G [auth E](5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid
C23 H37 N O5 S
OTZRAYGBFWZKMX-FRFVZSDQSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
F [auth E]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 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: 2025-04-09
    Type: Initial release
  • Version 2.0: 2025-05-28
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-04-22
    Changes: Data collection, Database references