[English] 日本語
Yorodumi
- EMDB-51502: Cryo EM structure of the E307T mutant of the human P2X4 receptor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51502
TitleCryo EM structure of the E307T mutant of the human P2X4 receptor in complex with the anthraquinone derivative PSB-0704
Map datamap sharpened with DeepEMhancer
Sample
  • Complex: human P2X4 receptor
    • Protein or peptide: P2X purinoceptor 4
  • Ligand: 1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsP2X4 / receptor / inhibitor / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory perception of touch / Platelet homeostasis / positive regulation of microglial cell migration / purinergic nucleotide receptor signaling pathway / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / negative regulation of cardiac muscle hypertrophy / ligand-gated calcium channel activity / Elevation of cytosolic Ca2+ levels / positive regulation of prostaglandin secretion ...sensory perception of touch / Platelet homeostasis / positive regulation of microglial cell migration / purinergic nucleotide receptor signaling pathway / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / negative regulation of cardiac muscle hypertrophy / ligand-gated calcium channel activity / Elevation of cytosolic Ca2+ levels / positive regulation of prostaglandin secretion / regulation of chemotaxis / tissue homeostasis / response to fluid shear stress / positive regulation of calcium ion transport / relaxation of cardiac muscle / positive regulation of endothelial cell chemotaxis / endothelial cell activation / response to ATP / cellular response to ATP / cellular response to zinc ion / behavioral response to pain / positive regulation of calcium ion transport into cytosol / positive regulation of blood vessel endothelial cell migration / membrane depolarization / regulation of cardiac muscle contraction / response to axon injury / Purinergic signaling in leishmaniasis infection / regulation of sodium ion transport / sensory perception of pain / positive regulation of calcium-mediated signaling / response to ischemia / apoptotic signaling pathway / calcium-mediated signaling / calcium ion transmembrane transport / regulation of blood pressure / positive regulation of nitric oxide biosynthetic process / cell junction / cell body / monoatomic ion transmembrane transport / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / cadherin binding / copper ion binding / signaling receptor binding / lysosomal membrane / perinuclear region of cytoplasm / signal transduction / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
P2X4 purinoceptor / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsNagel J / Vaaen V / Torp J / Geyer M / Claff T / Hagelueken G / Mueller CE
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1328 Germany
German Federal Ministry for Education and Research0315606B Germany
European Cooperation in Science and Technology (COST) actionCA21130European Union
CitationJournal: To Be Published
Title: Discovery of an allosteric P2X receptor binding site for anthraquinones by a chimeric approach combined with computational studies, bump-and-hole mutagenesis, and cryo-electron microscopy
Authors: Nagel J / Weinhausen S / Namasivayam V / Baqi Y / Al Musawi HAM / Abdelrahman A / Vaassen V / Schlegel J / Taplick L / Torp J / Kubicek J / Maertens B / Geyer M / Claff T / Hagelueken G / Mueller CE
History
DepositionSep 6, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51502.png

Downloads & links

-
Map

FileDownload / File: emd_51502.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap sharpened with DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 256 pix.
= 291.84 Å		1.14 Å/pix.
x 256 pix.
= 291.84 Å		1.14 Å/pix.
x 256 pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00701
Minimum - Maximum-0.005420963 - 2.0155416
Average (Standard dev.)0.002059661 (±0.031759087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: unsharpened map

Fileemd_51502_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Composite map calculated with phenix

Fileemd_51502_additional_2.map
AnnotationComposite map calculated with phenix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Overall reconstruction, sharpened with DeepEMhancer

Fileemd_51502_additional_3.map
AnnotationOverall reconstruction, sharpened with DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51502_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51502_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human P2X4 receptor

EntireName: human P2X4 receptor
Components
  • Complex: human P2X4 receptor
    • Protein or peptide: P2X purinoceptor 4
  • Ligand: 1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: human P2X4 receptor

SupramoleculeName: human P2X4 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: P2X purinoceptor 4

MacromoleculeName: P2X purinoceptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.303188 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGCCAALAA FLFEYDTPRI VLIRSRKVGL MNRAVQLLIL AYVIGWVFVW EKGYQETDSV VSSVTTKVKG VAVTRTSKLG FRIWDVADY VIPAQEENSL FVMTNVILTM NQTQGLCPEI PDATTVCKSD ASCTAGSAGT HSNGVSTGRC VAFNGSVKTC E VAAWCPVE ...String:
MAGCCAALAA FLFEYDTPRI VLIRSRKVGL MNRAVQLLIL AYVIGWVFVW EKGYQETDSV VSSVTTKVKG VAVTRTSKLG FRIWDVADY VIPAQEENSL FVMTNVILTM NQTQGLCPEI PDATTVCKSD ASCTAGSAGT HSNGVSTGRC VAFNGSVKTC E VAAWCPVE DDTHVPQPAF LKAAERFTLL VKNNIWYPKF NFSKRNILPN ITTTYLKSCI YDAKTDPFCP IFRLGKIVEN AG HSFQDMA VEGGIMGIQV NWDCNLDRAA SLCLPRYSFR RLDTRDVEHN VSPGYNFRFA KYYRDLAGNT QRTLIKAYGI RFD IIVFGK AGKFDIIPTM INIGSGLALL GMATVLCDII VLYCMKKRLY YREKKYKYVE DYEQGLASEL DQGSSGEFLE VLFQ GPHHH HHHHHHH

UniProtKB: P2X purinoceptor 4

-
Macromolecule #3: 1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxid...

MacromoleculeName: 1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid
type: ligand / ID: 3 / Number of copies: 3 / Formula: A1INJ
Molecular weightTheoretical: 493.467 Da

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79284
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