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- PDB-9jqy: Structural Insights into Selective Antagonism of TG6-129 and EP4 ... -

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Basic information

Entry
Database: PDB / ID: 9jqy
TitleStructural Insights into Selective Antagonism of TG6-129 and EP4 Prostaglandin Receptor
Components
  • GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / response to mechanical stimulus / response to prostaglandin E / JNK cascade ...negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / response to mechanical stimulus / response to prostaglandin E / JNK cascade / ERK1 and ERK2 cascade / positive regulation of cytokine production / cellular response to mechanical stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / bone development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response / cellular response to prostaglandin E stimulus / positive regulation of cytosolic calcium ion concentration / G alpha (s) signalling events / immune response / inflammatory response / membrane / plasma membrane
Similarity search - Function
Prostanoid EP4 receptor / Prostaglandin DP receptor / Prostanoid receptor / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Prostaglandin E2 receptor EP4 subtype
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsWu, Y.L. / Zhang, H. / Xu, J.Y. / Wu, C.R. / Xu, E.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural Insights into Selective and Dual Antagonism of EP2 and EP4 Prostaglandin Receptor
Authors: Wu, Y.L. / Zhang, H. / Xu, J.Y. / Wu, K. / Hu, W. / Wu, C.R. / Xu, E.H.
History
DepositionSep 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data 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
H: Heavy chain of Fab fragment
L: Light chain of Fab fragment
A: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4764
Polymers117,9823
Non-polymers4941
Water1086
1


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

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Components

#1: Antibody Heavy chain of Fab fragment


Mass: 27574.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody Light chain of Fab fragment


Mass: 28944.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype / prostaglandin E receptor EP4 / PGE receptor EP4 subtype / PGE2 receptor EP4 subtype / Prostanoid EP4 receptor


Mass: 61463.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human)
Gene: PTGER4, PTGER2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35408
#4: Chemical ChemComp-A1EC5 / ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide


Mass: 493.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20FN5O3S3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: human prostaglandin E receptor EP4 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Mus musculus (house mouse)10090
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.3
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97395 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025480
ELECTRON MICROSCOPYf_angle_d0.4027466
ELECTRON MICROSCOPYf_dihedral_angle_d9.8081929
ELECTRON MICROSCOPYf_chiral_restr0.037861
ELECTRON MICROSCOPYf_plane_restr0.004920

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