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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: To Be Published
Title: Local refinement of maleic acid bound OXGR1
Authors: Liu H / Zhang X / Xu HE
History
DepositionMay 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64588_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64588_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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