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- EMDB-61763: Structural Insights into Selective Antagonism of TG6-129 and EP2 ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61763
TitleStructural Insights into Selective Antagonism of TG6-129 and EP2 Prostaglandin Receptor
Map data
Sample
  • Complex: human prostaglandin E receptor EP2
    • Protein or peptide: Light chain of Fab fragment
    • Protein or peptide: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562
    • Protein or peptide: Heavy chain of Fab fragment
    • Protein or peptide: Nb
  • Ligand: ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide
KeywordsGPCR / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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 speciesHomo sapiens (human) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWu YL / Zhang H / Xu JY / Wu CR / Xu EH
Funding support China, 1 items
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 YL / Zhang H / Xu JY / Wu K / Hu W / Wu CR / Xu EH
History
DepositionSep 29, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61763.png

Downloads & links

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Map

FileDownload / File: emd_61763.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.5595094 - 2.4485223
Average (Standard dev.)-0.00022946077 (±0.04659465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61763_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61763_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 : human prostaglandin E receptor EP2

EntireName: human prostaglandin E receptor EP2
Components
  • Complex: human prostaglandin E receptor EP2
    • Protein or peptide: Light chain of Fab fragment
    • Protein or peptide: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562
    • Protein or peptide: Heavy chain of Fab fragment
    • Protein or peptide: Nb
  • Ligand: ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide

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Supramolecule #1: human prostaglandin E receptor EP2

SupramoleculeName: human prostaglandin E receptor EP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 ...

MacromoleculeName: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562,Prostaglandin E2 receptor EP2 subtype,Soluble cytochrome b562
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.678398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAKH HHHHHHHHAS VIKPEMKIKL RMEGAVNGHK FVIEGEGIGK PYEGTQTLDL TVEEGAPLPF SYDILTPAFQ YGNRAFTKY PEDIPDYFKQ AFPEGYSWER SMTYEDQGIC IATSDITMEG DCFFYEIRFD GTNFPPNGPV MQKKTLKWEP S TEKMYVED ...String:
DYKDDDDAKH HHHHHHHHAS VIKPEMKIKL RMEGAVNGHK FVIEGEGIGK PYEGTQTLDL TVEEGAPLPF SYDILTPAFQ YGNRAFTKY PEDIPDYFKQ AFPEGYSWER SMTYEDQGIC IATSDITMEG DCFFYEIRFD GTNFPPNGPV MQKKTLKWEP S TEKMYVED GVLKGDVEMA LLLEGGGHYR CDFKTTYKAK KDVRLPDAHE VDHRIEILSH DKDYNKVRLY EHAEARYSGG GS GGGGSAM GNASNDSQSE DCETRQWLPP GESPAISSVM FSAGVLGNLI ALALLARRWR GDVGCSAGRR SSLSLFHVLV TEL VFTDLL GTCLISPVVL ASYARNQTLV ALAPESRACT YFAFAMTFFS LATMLMLFAM ALERYLSIGH PYFYQRRVSR SGGL AVLPV IYAVSLLFCS LPLLDYGQYV QYCPGTWCFI RHGRTAYLQL YATLLLLLIV SVLACNFSVI LNLIRARRQL ADLED NWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKGGSGGRS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAA EQL KTTRNAYIQK YLERARSTLA EETDHLILLA IMTITFAVCS LPFTIFAYMN ETSSRKEKWD LQALRFLSIN SIIDPWV FA ILRPPVLRLM RSVLCCRISL RTQDATQTSC STQSDASKQA DL

UniProtKB: Prostaglandin E2 receptor EP2 subtype, Soluble cytochrome b562, Prostaglandin E2 receptor EP2 subtype

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Macromolecule #2: Heavy chain of Fab fragment

MacromoleculeName: Heavy chain of Fab fragment / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.152984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEVQLVESGG GLVQPGGSLR LSCAASGFNV RSFSIHWVRQ APGKGLEWVA YISSSSGSTS YADSVKGRFT ISADTSKNTA YLQMNSLRA EDTAVYYCAR WGYWPGEPWW KAFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
MEVQLVESGG GLVQPGGSLR LSCAASGFNV RSFSIHWVRQ APGKGLEWVA YISSSSGSTS YADSVKGRFT ISADTSKNTA YLQMNSLRA EDTAVYYCAR WGYWPGEPWW KAFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKS

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Macromolecule #3: Nb

MacromoleculeName: Nb / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.276541 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGRT ISRYAMSWFR QAPGKEREFV AVARRSGDGA FYADSVQGRF TVSRDDAKTV YLQMNSLKP EDTAVYYCAI DSDTFYSGSY DYWGQGTQVT VSS

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Macromolecule #4: Light chain of Fab fragment

MacromoleculeName: Light chain of Fab fragment / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.398066 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
MDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYLYYSLVT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRG

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Macromolecule #5: ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamo...

MacromoleculeName: ~{N}-[[4-[(5-ethyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl]carbamothioyl]-3-(4-fluorophenyl)propanamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1EC5
Molecular weightTheoretical: 493.598 Da

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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: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174481
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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