[English] 日本語
Yorodumi
- EMDB-61762: Structural Insights into Selective Antagonism of PF04418948 and E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61762
TitleStructural Insights into Selective Antagonism of PF04418948 and EP2 Prostaglandin Receptor
Map data
Sample
  • Complex: human prostaglandin E receptor EP2
    • 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: Light chain of Fab fragment
    • Protein or peptide: Nb
  • Ligand: 1-(4-fluorophenyl)carbonyl-3-[(6-methoxynaphthalen-2-yl)oxymethyl]azetidine-3-carboxylic acid
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: 3.5 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

-
Structure visualization

Supplemental images

emd_61762.png

Downloads & links

-
Map

FileDownload / File: emd_61762.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-2.0324788 - 3.3316088
Average (Standard dev.)0.0010550761 (±0.060139176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.616 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61762_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61762_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human prostaglandin E receptor EP2

EntireName: human prostaglandin E receptor EP2
Components
  • Complex: human prostaglandin E receptor EP2
    • 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: Light chain of Fab fragment
    • Protein or peptide: Nb
  • Ligand: 1-(4-fluorophenyl)carbonyl-3-[(6-methoxynaphthalen-2-yl)oxymethyl]azetidine-3-carboxylic acid

-
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)

-
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: 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

-
Macromolecule #2: Light chain of Fab fragment

MacromoleculeName: Light 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: 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

-
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

-
Macromolecule #4: 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: 4 / 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

-
Macromolecule #5: 1-(4-fluorophenyl)carbonyl-3-[(6-methoxynaphthalen-2-yl)oxymethyl...

MacromoleculeName: 1-(4-fluorophenyl)carbonyl-3-[(6-methoxynaphthalen-2-yl)oxymethyl]azetidine-3-carboxylic acid
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1ECS
Molecular weightTheoretical: 409.407 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 214366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more