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- PDB-9uxq: Local refinement of AKG bound OXGR1 -

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Basic information

Entry
Database: PDB / ID: 9uxq
TitleLocal refinement of AKG bound OXGR1
Components2-oxoglutarate receptor 1
KeywordsSIGNALING PROTEIN / 2-oxoglutarate / AKG / 2-oxoglutarate receptor 1 / OXGR1 / cryo-EM / membrane protein
Function / homology
Function and homology information


Class A/1 (Rhodopsin-like receptors) / G protein-coupled receptor activity / signaling receptor activity / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G protein-coupled receptor signaling pathway / innate immune response / membrane / plasma membrane
Similarity search - Function
7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / 2-oxoglutarate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLiu, H. / Zhang, X. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2026
Title: Molecular architecture of OXGR1 reveals an evolutionary conserved mechanisms for metabolite surveillance.
Authors: Xinyue Zhang / Yujie Lu / Xinheng He / Shimeng Guo / Changyao Li / Yu Wang / Yuan Gao / Juxia Yao / Qingning Yuan / Yinshan Tang / Jing Hu / Wen Hu / Zijuan Luo / Kai Wu / Yue Wang / Wanchao ...Authors: Xinyue Zhang / Yujie Lu / Xinheng He / Shimeng Guo / Changyao Li / Yu Wang / Yuan Gao / Juxia Yao / Qingning Yuan / Yinshan Tang / Jing Hu / Wen Hu / Zijuan Luo / Kai Wu / Yue Wang / Wanchao Yin / Xin Xie / H Eric Xu / Heng Liu /
Abstract: The ability of cells to sense and respond to metabolic signals is fundamental to life, yet the molecular mechanisms underlying metabolite surveillance remain incompletely understood. Here, we ...The ability of cells to sense and respond to metabolic signals is fundamental to life, yet the molecular mechanisms underlying metabolite surveillance remain incompletely understood. Here, we elucidate the structural basis of metabolite recognition by OXGR1, a G Protein-Coupled Receptor (GPCR) that senses key intermediates in the tricarboxylic acid (TCA) cycle. Using cryo-electron microscopy, we determined cryo-EM structures of OXGR1 bound to α-ketoglutarate (AKG), itaconate (ITA), and structurally related metabolites succinate (SUC) and maleate (MA). These structures reveal a positively charged binding pocket and an extensive hydrogen-bond network that mediate selective recognition of dicarboxylic acids. In addition, we identify a distinct arrangement of hydrophobic residues that modulates ligand potency and selectivity. Mutational analysis and molecular dynamics simulations further demonstrate that noncanonical micro-switch motifs, including FRY and NLxxY, are essential for ligand recognition and receptor activation. Comparative structural and evolutionary analyses indicate that these mechanisms are conserved across species, underscoring the critical role of OXGR1 in maintaining metabolic homeostasis. Together, our findings define a mechanistic framework for metabolite sensing by OXGR1 and provide a framework for therapeutic modulation of metabolic and inflammatory diseases.
History
DepositionMay 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: 2-oxoglutarate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4302
Polymers38,2841
Non-polymers1461
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 2-oxoglutarate receptor 1 / Alpha-ketoglutarate receptor 1 / G-protein coupled receptor 80 / G-protein coupled receptor 99 / ...Alpha-ketoglutarate receptor 1 / G-protein coupled receptor 80 / G-protein coupled receptor 99 / P2Y purinoceptor 15 / P2Y15 / P2Y-like GPCR / P2Y-like nucleotide receptor


Mass: 38284.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OXGR1, GPR80, GPR99, P2RY15, P2Y15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96P68
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AKG bound OXGR1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405687 / Symmetry type: POINT
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032366
ELECTRON MICROSCOPYf_angle_d0.5523226
ELECTRON MICROSCOPYf_dihedral_angle_d6.033314
ELECTRON MICROSCOPYf_chiral_restr0.04395
ELECTRON MICROSCOPYf_plane_restr0.004385

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