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- EMDB-65376: The structure of ITN bound OXGR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-65376
TitleThe structure of ITN bound OXGR1
Map data
Sample
  • Complex: ITN bound OXGR1
    • Protein or peptide: Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Fusion protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Fusion protein,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Gq alpha
    • Protein or peptide: scFv-16
  • Ligand: 2-methylidenebutanedioic acid
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


Class A/1 (Rhodopsin-like receptors) / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...Class A/1 (Rhodopsin-like receptors) / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / electron transport chain / G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / outer membrane-bounded periplasmic space / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / G-protein beta-subunit binding / extracellular vesicle / sensory perception of taste / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / signaling receptor activity / retina development in camera-type eye / fibroblast proliferation / GTPase binding / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / periplasmic space / electron transfer activity / cell population proliferation / Extra-nuclear estrogen signaling / iron ion binding / G protein-coupled receptor signaling pathway / innate immune response / lysosomal membrane / GTPase activity / heme binding / DNA damage response / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Bacterial extracellular solute-binding protein / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Bacterial extracellular solute-binding protein / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Soluble cytochrome b562 / Maltose/maltodextrin-binding periplasmic protein / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / 2-oxoglutarate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli K-12 (bacteria) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsSu Q / Liang EY / Ma TS / Chen ZY / Tang XF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The structure of ITN bound OXGR1
Authors: Su Q / Liang EY / Ma TS / Chen ZY / Tang XF
History
DepositionJul 14, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65376.png

Downloads & links

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Map

FileDownload / File: emd_65376.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 324 pix.
= 303.264 Å		0.94 Å/pix.
x 324 pix.
= 303.264 Å		0.94 Å/pix.
x 324 pix.
= 303.264 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.0018094323 - 1.785986
Average (Standard dev.)0.0006379976 (±0.017930495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 303.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65376_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65376_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : ITN bound OXGR1

EntireName: ITN bound OXGR1
Components
  • Complex: ITN bound OXGR1
    • Protein or peptide: Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Fusion protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Fusion protein,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Gq alpha
    • Protein or peptide: scFv-16
  • Ligand: 2-methylidenebutanedioic acid

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Supramolecule #1: ITN bound OXGR1

SupramoleculeName: ITN bound OXGR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochr...

MacromoleculeName: Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Fusion protein,Maltose/maltodextrin-binding ...Name: Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Soluble cytochrome b562,2-oxoglutarate receptor 1,Fusion protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 154.29775 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LGSMNEPLDY LANASDFPDY A AAFGNCTD ...String:
MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LGSMNEPLDY LANASDFPDY A AAFGNCTD ENIPLKMHYL PVIYGIIFLV GFPGNAVVIS TYIFKMRPWK SSTIIMLNLA CTDLLYLTSL PFLIHYYASG EN WIFGDFM CKFIRFSFHF NLYSSILFLT CFSIFRYCVI IHPMSCFSIH KTRCAVVACA VVWIISLVAV IPMTFLITST NRT NRSACL DLTSSDELNT IKWYNLILTA TTFCLPLVIV TLCYTTIIHT LTHGLQTDSC LKQKARRLTI LLLLAFYVCF LPFH ILRVI RIESRLLSIS CSIENQIHEA YIVSRPLAAL NTFGNLLLYV VVSDNFQQAV CSTVRCKVSG NLEQAKKISY SNNPM VFTL EDFVGDWEQT AAYNLDQVLE QGGVSSLLQN LAVSVTPIQR IVRSGENALK IDIHVIIPYE GLSADQMAQI EEVFKV VYP VDDHHFKVIL PYGTLVIDGV TPNMLNYFGR PYEGIAVFDG KKITVTGTLW NGNKIIDERL ITPDGSMLFR VTINSGG GS GGDEVDAGGS MAKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDR F GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNGKLIAYP IAVEALSLIY NKDLLPNPPK TWEEIPALDK ELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDVGVDNA GAKAGLTFLV DLIKNKHMNA DTDYSIAEAA FNKGETAMTI NGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGVLSAG INAASPNKEL AKEFLENYLL TDEGLEAVNK DKPLGAVALK S YEEELAKD PRIAATMENA QKGEIMPNIP QMSAFWYAVR TAVINAASGR QTVDEALKDA QTGGGGSGGG GSMAKIEEGK LV IWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE KFPQVAATGD GPDIIFWAHD RFGGYAQSGL LAEITPDKAF QDK LYPFTW DAVRYNGKLI AYPIAVEALS LIYNKDLLPN PPKTWEEIPA LDKELKAKGK SALMFNLQEP YFTWPLIAAD GGYA FKYEN GKYDIKDVGV DNAGAKAGLT FLVDLIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLP TFKG QPSKPFVGVL SAGINAASPN KELAKEFLEN YLLTDEGLEA VNKDKPLGAV ALKSYEEELA KDPRIAATME NAQKGE IMP NIPQMSAFWY AVRTAVINAA SGRQTVDEAL KDAQT

UniProtKB: Soluble cytochrome b562, 2-oxoglutarate receptor 1, Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #3: Fusion protein,Guanine nucleotide-binding protein G(I)/G(S)/G(T) ...

MacromoleculeName: Fusion protein,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.900766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSKGEEENM ASTPFKFQLK GTINGKSFTV EGEGEGNSHE GSHKGKYVCT SGKLPMSWAA LGTTFGYGMK YYTKYPSGLK NWFREVMPG GFTYDRHIQY KGDGSIHAKH QHFMKNGTYH NIVEFTGQDF KENSPVLTGD MNVSLPNEVP QIPRDDGVEC P VTLLYPLL ...String:
MVSKGEEENM ASTPFKFQLK GTINGKSFTV EGEGEGNSHE GSHKGKYVCT SGKLPMSWAA LGTTFGYGMK YYTKYPSGLK NWFREVMPG GFTYDRHIQY KGDGSIHAKH QHFMKNGTYH NIVEFTGQDF KENSPVLTGD MNVSLPNEVP QIPRDDGVEC P VTLLYPLL SDKSKYVEAH QYTICKPLHN QPAPDVPYHW IRKQYTQSKD DAEERDHICQ SETLEAHLKG MDELYKGGGG SG GGSMSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDG KLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD DNQI VTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CFFPN GNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADRAGVLAGH DNRVSC LGV TDDGMAVATG SWDSFLKIWN GSSGGGGSGG GGSSGVSGWR LFKKIS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Gq alpha

MacromoleculeName: Gq alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.724383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF KSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRKEFVDIST ASG DGRHIC YPHFTCSVDT ENARRIFNDC KDIILQMNLR EYNLV

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Macromolecule #5: scFv-16

MacromoleculeName: scFv-16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 59.466527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLSGA RCDVQLVESG GGLVQPGGSR KLSCSASGFA FSSFGMHWVR QAPEKGLEWV AYISSGSGTI YYADTVKGR FTISRDDPKN TLFLQMTSLR SEDTAMYYCV RSIYYYGSSP FDFWGQGTTL TVSAGGGGSG GGGSGGGGSA D IVMTQATS ...String:
MDMRVPAQLL GLLLLWLSGA RCDVQLVESG GGLVQPGGSR KLSCSASGFA FSSFGMHWVR QAPEKGLEWV AYISSGSGTI YYADTVKGR FTISRDDPKN TLFLQMTSLR SEDTAMYYCV RSIYYYGSSP FDFWGQGTTL TVSAGGGGSG GGGSGGGGSA D IVMTQATS SVPVTPGESV SISCRSSKSL LHSNGNTYLY WFLQRPGQSP QLLIYRMSNL ASGVPDRFSG SGSGTAFTLT IS RLEAEDV GVYYCMQHLE YPLTFGAGTK LELGGGSMDS TEAVIKEFMR FKVHMEGSMN GHEFEIEGEG EGRPYEGTQT AKL KVTKGG PLPFSWDILS PQFMYGSRAF IKHPADIPDY WKQSFPEGFK WERVMIFEDG GTVSVTQDTS LEDGTLIYKV KLRG GNFPP DGPVMQKRTM GWEASTERLY PEDVVLKGDI KMALRLKDGG RYLADFKTTY KAKKPVQMPG AFNIDRKLDI TSHNE DYTV VEQYERSVAR HSTGGSGGSA AAWSHPQFEK GGGSGGGSGG SAWSHPQFEK GGGGSHHHHH HHH

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Macromolecule #6: 2-methylidenebutanedioic acid

MacromoleculeName: 2-methylidenebutanedioic acid / type: ligand / ID: 6 / Number of copies: 1 / Formula: ITN
Molecular weightTheoretical: 130.099 Da
Chemical component information

ChemComp-ITN:
2-methylidenebutanedioic acid

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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: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON I (4k 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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 334276
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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