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- EMDB-64588: Local refinement of maleic acid bound OXGR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64588
TitleLocal refinement of maleic acid bound OXGR1
Map data
Sample
  • Complex: maleic acid bound OXGR1
    • Protein or peptide: 2-oxoglutarate receptor 1
  • Ligand: MALEIC ACID
  • Ligand: water
Keywordsmaleic acid / MA / 2-oxoglutarate receptor 1 / OXGR1 / cryo-EM / membrane protein / SIGNALING 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-oxoglutarate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLiu H / Zhang X / Xu HE
Funding support China, 1 items
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, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64588.png

Downloads & links

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Map

FileDownload / File: emd_64588.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.457738 - 5.7339616
Average (Standard dev.)0.00009225184 (±0.10003099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64588_msk_1.map
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Half map: #1

Fileemd_64588_half_map_1.map
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Half map: #2

Fileemd_64588_half_map_2.map
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Sample components

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Entire : maleic acid bound OXGR1

EntireName: maleic acid bound OXGR1
Components
  • Complex: maleic acid bound OXGR1
    • Protein or peptide: 2-oxoglutarate receptor 1
  • Ligand: MALEIC ACID
  • Ligand: water

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Supramolecule #1: maleic acid bound OXGR1

SupramoleculeName: maleic acid bound OXGR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 2-oxoglutarate receptor 1

MacromoleculeName: 2-oxoglutarate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.28402 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNEPLDYLAN ASDFPDYAAA FGNCTDENIP LKMHYLPVIY GIIFLVGFPG NAVVISTYIF KMRPWKSSTI IMLNLACTDL LYLTSLPFL IHYYASGENW IFGDFMCKFI RFSFHFNLYS SILFLTCFSI FRYCVIIHPM SCFSIHKTRC AVVACAVVWI I SLVAVIPM ...String:
MNEPLDYLAN ASDFPDYAAA FGNCTDENIP LKMHYLPVIY GIIFLVGFPG NAVVISTYIF KMRPWKSSTI IMLNLACTDL LYLTSLPFL IHYYASGENW IFGDFMCKFI RFSFHFNLYS SILFLTCFSI FRYCVIIHPM SCFSIHKTRC AVVACAVVWI I SLVAVIPM TFLITSTNRT NRSACLDLTS SDELNTIKWY NLILTATTFC LPLVIVTLCY TTIIHTLTHG LQTDSCLKQK AR RLTILLL LAFYVCFLPF HILRVIRIES RLLSISCSIE NQIHEAYIVS RPLAALNTFG NLLLYVVVSD NFQQAVCSTV RCK VSGNLE QAKKISYSNN P

UniProtKB: 2-oxoglutarate receptor 1

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Macromolecule #2: MALEIC ACID

MacromoleculeName: MALEIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: MAE
Molecular weightTheoretical: 116.072 Da
Chemical component information

ChemComp-MAE:
MALEIC ACID

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 436647
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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