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- PDB-9gp7: Cryo EM structure of the E307T mutant of the human P2X4 receptor ... -

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Basic information

Entry
Database: PDB / ID: 9gp7
TitleCryo EM structure of the E307T mutant of the human P2X4 receptor in complex with the anthraquinone derivative PSB-0704
ComponentsP2X purinoceptor 4
KeywordsMEMBRANE PROTEIN / P2X4 / receptor / inhibitor
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
: / P2X purinoceptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsNagel, J. / Vaaen, V. / Torp, J. / Geyer, M. / Claff, T. / Hagelueken, G. / Mueller, C.E.
Funding support Germany, European Union, 3items
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, H.A.M. / Abdelrahman, A. / Vaassen, V. / Schlegel, J. / Taplick, L. / Torp, J. / Kubicek, J. / Maertens, B. / Geyer, M. / ...Authors: Nagel, J. / Weinhausen, S. / Namasivayam, V. / Baqi, Y. / Al Musawi, H.A.M. / Abdelrahman, A. / Vaassen, V. / Schlegel, J. / Taplick, L. / Torp, J. / Kubicek, J. / Maertens, B. / Geyer, M. / Claff, T. / Hagelueken, G. / Mueller, C.E.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 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
A: P2X purinoceptor 4
B: P2X purinoceptor 4
C: P2X purinoceptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32712
Polymers138,9103
Non-polymers3,4179
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein P2X purinoceptor 4 / P2X4 / ATP receptor / Purinergic receptor


Mass: 46303.188 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99571
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-A1INJ / 1-azanyl-4-[(3-carboxy-4-phenylazanyl-phenyl)amino]-9,10-bis(oxidanylidene)anthracene-2-carboxylic acid


Mass: 493.467 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H19N3O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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 P2X4 receptor / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79284 / Symmetry type: POINT

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