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- EMDB-61744: Structural Insights into Selective Antagonism Grapiprant and EP4 ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61744
TitleStructural Insights into Selective Antagonism Grapiprant and EP4 Prostaglandin Receptor
Map data
Sample
  • Complex: human prostaglandin E receptor EP4
    • Protein or peptide: Heavy chain of Fab fragment
    • Protein or peptide: Light chain of Fab fragment
  • Protein or peptide: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
  • Ligand: 1-[2-[4-(2-ethyl-4,6-dimethyl-imidazo[4,5-c]pyridin-1-yl)phenyl]ethyl]-3-(4-methylphenyl)sulfonyl-urea
  • Ligand: water
KeywordsGPCR / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 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 28, 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_61744.png

Downloads & links

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Map

FileDownload / File: emd_61744.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.)
0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å		0.82 Å/pix.
x 320 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.5133815 - 4.3343606
Average (Standard dev.)-0.0009288613 (±0.07703866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61744_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_61744_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 EP4

EntireName: human prostaglandin E receptor EP4
Components
  • Complex: human prostaglandin E receptor EP4
    • Protein or peptide: Heavy chain of Fab fragment
    • Protein or peptide: Light chain of Fab fragment
  • Protein or peptide: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
  • Ligand: 1-[2-[4-(2-ethyl-4,6-dimethyl-imidazo[4,5-c]pyridin-1-yl)phenyl]ethyl]-3-(4-methylphenyl)sulfonyl-urea
  • Ligand: water

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Supramolecule #1: human prostaglandin E receptor EP4

SupramoleculeName: human prostaglandin E receptor EP4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Heavy chain of Fab fragment

MacromoleculeName: Heavy chain of Fab fragment / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.574092 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEWRWIFLFL LSGTTGVHSE IQLQQSGPEL VKPGASVKVS CKASGFPFST YNIYWVIQSH GKSLEWIGYI DPYNGGTSYN QKFRGKATL TVDKSSSTAY MHLNSLTSED SAVYYCARRW YTYDGDWFAY WGQGTLVTVS AAKTTAPSVY PLAPVCGDTT G SSVTLGCL ...String:
MEWRWIFLFL LSGTTGVHSE IQLQQSGPEL VKPGASVKVS CKASGFPFST YNIYWVIQSH GKSLEWIGYI DPYNGGTSYN QKFRGKATL TVDKSSSTAY MHLNSLTSED SAVYYCARRW YTYDGDWFAY WGQGTLVTVS AAKTTAPSVY PLAPVCGDTT G SSVTLGCL VKGYFPEPVT LTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PR GPTIKPC PPCKCP

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Macromolecule #2: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 ...

MacromoleculeName: GFP-like fluorescent chromoprotein,Prostaglandin E2 receptor EP4 subtype
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.463859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ASVIKPEMKI KLRMEGAVNG HKFVIEGEGI GKPYEGTQTL DLTVEEGAPL PFSYDILTPA FQYGNRAFTK YPEDIPDYFK QAFPEGYSW ERSMTYEDQG ICIATSDITM EGDCFFYEIR FDGTNFPPNG PVMQKKTLKW EPSTEKMYVE DGVLKGDVEM A LLLEGGGH ...String:
ASVIKPEMKI KLRMEGAVNG HKFVIEGEGI GKPYEGTQTL DLTVEEGAPL PFSYDILTPA FQYGNRAFTK YPEDIPDYFK QAFPEGYSW ERSMTYEDQG ICIATSDITM EGDCFFYEIR FDGTNFPPNG PVMQKKTLKW EPSTEKMYVE DGVLKGDVEM A LLLEGGGH YRCDFKTTYK AKKDVRLPDA HEVDHRIEIL SHDKDYNKVR LYEHAEARYS GGGSGGGGSA PGVQSSASLS PD RLNSPVT IPAVMFIFGV VGNLVAIVVL CKSRKEQKET TFYTLVCGLL VTDLLGTLLV SPVTIATYMK GQWPGGQPLC EYS TFILLF FSLSRLSIIC AMSVERYLAI NHAYFYSHYV DKRLAGLTLF AVYASNVLFC ALPNMGLGSS RLQYPDTWCF IDWT TQVTA HAAYSYMYAG FSSFLILATV LCNVLVCGAL LRMHRQFFRR IAGAEIQMVI LLIATSLVVL ICSIPLVVRV FVNQL YQPS LEREVSKNPD LQAIRIASVN PILDPWIYIL LRKTVLSKAI EKIKCLFCRI GGSRRERSGQ HCSDS

UniProtKB: Prostaglandin E2 receptor EP4 subtype

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Macromolecule #3: Light chain of Fab fragment

MacromoleculeName: Light chain of Fab fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.944303 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDMRTPAQFL GILLLWFPGI KCDIKMTQSP SSMYVSLGER VTITCKASQD INRYLSWFQQ KPGKSPKTLI YRANRMLDGV PSRFSGSGS GQDYSLTISS LEYEDMGNYY CLQYDEFPFT FGSGTKLEIK RADAAPTVSI FPPSSEQLTS GGASVVCFLN N FYPKDINV ...String:
MDMRTPAQFL GILLLWFPGI KCDIKMTQSP SSMYVSLGER VTITCKASQD INRYLSWFQQ KPGKSPKTLI YRANRMLDGV PSRFSGSGS GQDYSLTISS LEYEDMGNYY CLQYDEFPFT FGSGTKLEIK RADAAPTVSI FPPSSEQLTS GGASVVCFLN N FYPKDINV KWKIDGSERQ NGVLNSWTDQ DSKDSTYSMS STLTLTKDEY ERHNSYTCEA THKTSTSPIV KSFNRNECVD EN LYFQGAS HHHHHHHH

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Macromolecule #4: 1-[2-[4-(2-ethyl-4,6-dimethyl-imidazo[4,5-c]pyridin-1-yl)phenyl]e...

MacromoleculeName: 1-[2-[4-(2-ethyl-4,6-dimethyl-imidazo[4,5-c]pyridin-1-yl)phenyl]ethyl]-3-(4-methylphenyl)sulfonyl-urea
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1ECR
Molecular weightTheoretical: 491.605 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287641
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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