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- PDB-8zt2: Structure of calcium preference ATP-gated channel Apo-P2X1 in the... -

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Basic information

Entry
Database: PDB / ID: 8zt2
TitleStructure of calcium preference ATP-gated channel Apo-P2X1 in the Desensitized state 1
ComponentsP2X purinoceptor 1
KeywordsTRANSPORT PROTEIN / ion channel
Function / homology
Function and homology information


Platelet homeostasis / Elevation of cytosolic Ca2+ levels / insemination / positive regulation of monoatomic ion transport / positive regulation of calcium ion import across plasma membrane / suramin binding / serotonin secretion by platelet / regulation of vascular associated smooth muscle contraction / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity ...Platelet homeostasis / Elevation of cytosolic Ca2+ levels / insemination / positive regulation of monoatomic ion transport / positive regulation of calcium ion import across plasma membrane / suramin binding / serotonin secretion by platelet / regulation of vascular associated smooth muscle contraction / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / regulation of presynaptic cytosolic calcium ion concentration / regulation of smooth muscle contraction / ceramide biosynthetic process / ligand-gated calcium channel activity / regulation of synaptic vesicle exocytosis / response to ATP / regulation of calcium ion transport / monoatomic cation transmembrane transport / regulation of vasoconstriction / monoatomic cation channel activity / monoatomic ion transport / neuronal action potential / Neutrophil degranulation / presynaptic active zone membrane / synaptic transmission, glutamatergic / platelet activation / regulation of blood pressure / calcium ion transmembrane transport / monoatomic ion transmembrane transport / postsynaptic membrane / membrane raft / external side of plasma membrane / nucleotide binding / apoptotic process / protein-containing complex binding / glutamatergic synapse / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
P2X1 purinoceptor / : / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / P2X purinoceptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsZhang, H. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2026
Title: Structural basis for a central permeation pathway in the P2X1 receptor.
Authors: Heng Zhang / Pengpeng Wu / Zhiyong Gu / Youwei Xu / Wen Hu / Qingning Yuan / Bingqing Xia / H Eric Xu / Zhaobing Gao /
Abstract: The ion permeation pathway is a critical determinant of ion channel function and selectivity; however, the structural basis for ion permeation in the P2X1 receptor, an ATP-gated ion channel crucial ...The ion permeation pathway is a critical determinant of ion channel function and selectivity; however, the structural basis for ion permeation in the P2X1 receptor, an ATP-gated ion channel crucial for platelet activation, thrombosis, and male infertility, remains incompletely understood. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the P2X1 receptor, which reveal a central ion permeation pathway spanning the entire extracellular domain, complementing the existing paradigms of ion channel architecture for the P2X receptor family. Within this pathway, we identify specific sites that coordinate hydrated calcium ions, including an aspartate ring that acts as a selectivity filter at the apex of the central vestibule. We also discover that a small molecule, 3,5-bis(trifluoromethyl)aniline, binds at the top of the central vestibule and potently inhibits cation flux through this central permeation pathway. Our findings reveal a new inhibitor-binding site in the P2X1 receptor. These insights provide a structural framework for the rational design of subtype-specific P2X receptor inhibitors targeting the central vestibule.
History
DepositionJun 6, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P2X purinoceptor 1
B: P2X purinoceptor 1
C: P2X purinoceptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,25919
Polymers145,6343
Non-polymers3,62516
Water1267
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

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Protein / Sugars , 2 types, 12 molecules ABC

#1: Protein P2X purinoceptor 1 / P2X1 / ATP receptor / Purinergic receptor


Mass: 48544.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: P2rx1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51576
#3: 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.: 9 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 4 types, 14 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: structure of Apo p2x1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200491 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028190
ELECTRON MICROSCOPYf_angle_d0.47611121
ELECTRON MICROSCOPYf_dihedral_angle_d13.862946
ELECTRON MICROSCOPYf_chiral_restr0.0431242
ELECTRON MICROSCOPYf_plane_restr0.0031398

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