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- PDB-9vv6: The structure of ITN bound OXGR1 -

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Basic information

Entry
Database: PDB / ID: 9vv6
TitleThe structure of ITN bound OXGR1
Components
  • 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
  • Gq alpha
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • 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
  • scFv-16
KeywordsMEMBRANE PROTEIN / GPCR
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
2-methylidenebutanedioic acid / 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 speciesEscherichia coli (E. coli)
Homo sapiens (human)
Escherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsSu, Q. / Liang, E.Y. / Ma, T.S. / Chen, Z.Y. / Tang, X.F.
Funding support China, 1items
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, E.Y. / Ma, T.S. / Chen, Z.Y. / Tang, X.F.
History
DepositionJul 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 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
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: 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
B: Gq alpha
E: scFv-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,3816
Polymers330,2515
Non-polymers1301
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules ACDB

#1: Protein 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 / Cytochrome b-562 / Alpha-ketoglutarate receptor 1 / G-protein coupled receptor 80 / G-protein ...Cytochrome b-562 / 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 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 154297.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: cybC, OXGR1, GPR80, GPR99, P2RY15, P2Y15, malE, b4034, JW3994
Production host: Homo sapiens (human)
References: UniProt: P0ABE7, UniProt: Q96P68, UniProt: P0AEX9
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Homo sapiens (human) / References: UniProt: P59768
#3: Protein 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 / Transducin beta chain 1


Mass: 66900.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Homo sapiens (human) / References: UniProt: P62873
#4: Protein Gq alpha


Mass: 41724.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody / Non-polymers , 2 types, 2 molecules E

#5: Antibody scFv-16


Mass: 59466.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#6: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4

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Details

Has ligand of interestN
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: ITN bound OXGR1 / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
5cryoSPARCCTF correction
13Coot3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334276 / Symmetry type: POINT
RefinementHighest resolution: 2.62 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039239
ELECTRON MICROSCOPYf_angle_d0.6412527
ELECTRON MICROSCOPYf_dihedral_angle_d4.6231255
ELECTRON MICROSCOPYf_chiral_restr0.0431429
ELECTRON MICROSCOPYf_plane_restr0.0041587

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