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- PDB-9x1d: apo structure of P2X332 -

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Basic information

Entry
Database: PDB / ID: 9x1d
Titleapo structure of P2X332
Components
  • P2X purinoceptor 2
  • P2X purinoceptor 3
KeywordsSIGNALING PROTEIN / P2X
Function / homology
Function and homology information


Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / Elevation of cytosolic Ca2+ levels / response to ATP / protein homotrimerization / cellular response to ATP / ligand-gated monoatomic ion channel activity / positive regulation of calcium ion transport into cytosol / response to ischemia ...Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / Elevation of cytosolic Ca2+ levels / response to ATP / protein homotrimerization / cellular response to ATP / ligand-gated monoatomic ion channel activity / positive regulation of calcium ion transport into cytosol / response to ischemia / neuronal dense core vesicle / sensory perception of sound / positive regulation of calcium-mediated signaling / hippocampal mossy fiber to CA3 synapse / transmembrane transport / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / calcium ion transmembrane transport / postsynapse / signaling receptor complex / apical plasma membrane / axon / neuronal cell body / signal transduction / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
P2X3 purinoceptor / P2X2 purinoceptor / : / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
P2X purinoceptor 3 / P2X purinoceptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, C. / Yu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure and gating mechanism of P2X2/P2X3 heteromer channels
Authors: Wang, C. / Yu, Y.
History
DepositionOct 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / 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 2
C: P2X purinoceptor 3
B: P2X purinoceptor 3


Theoretical massNumber of molelcules
Total (without water)140,4853
Polymers140,4853
Non-polymers00
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 2 / P2X2 / ATP receptor / Purinergic receptor


Mass: 51814.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX2, P2X2 / Production host: Homo sapiens (human) / References: UniProt: Q9UBL9
#2: Protein P2X purinoceptor 3 / P2X3 / ATP receptor / Purinergic receptor


Mass: 44334.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX3 / Production host: Homo sapiens (human) / References: UniProt: P56373
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: P2X332 apo form / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 6 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59230 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047797
ELECTRON MICROSCOPYf_angle_d0.69910565
ELECTRON MICROSCOPYf_dihedral_angle_d6.6271049
ELECTRON MICROSCOPYf_chiral_restr0.0471195
ELECTRON MICROSCOPYf_plane_restr0.0071335

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