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- PDB-9jro: Structural Insights into Selective Antagonism of PF04418948 and E... -

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Basic information

Entry
Database: PDB / ID: 9jro
TitleStructural Insights into Selective Antagonism of PF04418948 and EP2 Prostaglandin Receptor
Components
  • GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • Nb
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


prostaglandin E receptor activity / Prostanoid ligand receptors / response to nematode / response to progesterone / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to prostaglandin E stimulus / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / response to lipopolysaccharide ...prostaglandin E receptor activity / Prostanoid ligand receptors / response to nematode / response to progesterone / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to prostaglandin E stimulus / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / response to lipopolysaccharide / G alpha (s) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / heme binding / plasma membrane
Similarity search - Function
Prostanoid EP2 receptor / Prostanoid receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
: / Soluble cytochrome b562 / Prostaglandin E2 receptor EP2 subtype
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 29, 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
N: Nb
A: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9155
Polymers137,5064
Non-polymers4091
Water00
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: 24152.984 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: 23398.066 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 Nb


Mass: 13276.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562 / PGE receptor EP2 subtype / PGE2 receptor EP2 subtype / Prostanoid EP2 receptor / Cytochrome b-562


Mass: 76678.398 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. exp.) Escherichia coli (E. coli)
Gene: PTGER2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43116, UniProt: P0ABE7
#5: Chemical ChemComp-A1ECS / 1-(4-fluorophenyl)carbonyl-3-[(6-methoxynaphthalen-2-yl)oxymethyl]azetidine-3-carboxylic acid


Mass: 409.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20FNO5 / Feature type: SUBJECT OF INVESTIGATION
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 EP2 / Type: COMPLEX / Entity ID: #4, #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Escherichia coli (E. coli)562
41Mus 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 software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214366 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0017077
ELECTRON MICROSCOPYf_angle_d0.4129621
ELECTRON MICROSCOPYf_dihedral_angle_d17.082499
ELECTRON MICROSCOPYf_chiral_restr0.0361095
ELECTRON MICROSCOPYf_plane_restr0.0041208

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