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- EMDB-60447: Structure of calcium preference ATP-gated channel P2X1 in the Des... -

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Basic information

Entry
Database: EMDB / ID: EMD-60447
TitleStructure of calcium preference ATP-gated channel P2X1 in the Desensitized state 2 in the presence of 1mM Calcium ion
Map data
Sample
  • Complex: structure of Apo p2x1
    • Protein or peptide: P2X purinoceptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsion channel / TRANSPORT PROTEIN
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
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsZhang H / Xu HE
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60447.png

Downloads & links

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Map

FileDownload / File: emd_60447.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å		0.81 Å/pix.
x 256 pix.
= 207.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.7505935 - 1.9177562
Average (Standard dev.)0.0010471016 (±0.05179455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 207.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60447_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_60447_half_map_2.map
Projections & Slices
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Sample components

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Entire : structure of Apo p2x1

EntireName: structure of Apo p2x1
Components
  • Complex: structure of Apo p2x1
    • Protein or peptide: P2X purinoceptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: structure of Apo p2x1

SupramoleculeName: structure of Apo p2x1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: P2X purinoceptor 1

MacromoleculeName: P2X purinoceptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.908691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MARRLQDELS AFFFEYDTPR MVLVRNKKVG VIFRLIQLVV LVYVIGWVFV YEKGYQTSSG LISSVSVKLK GLAVTQLQGL GPQVWDVAD YVFPAHGDSS FVVMTNFIMT PQQAQGHCAE NPEGGICQDD SGCTPGKAER KAQGIRTGNC VPFNGTVKTC E IFGWCPVE ...String:
MARRLQDELS AFFFEYDTPR MVLVRNKKVG VIFRLIQLVV LVYVIGWVFV YEKGYQTSSG LISSVSVKLK GLAVTQLQGL GPQVWDVAD YVFPAHGDSS FVVMTNFIMT PQQAQGHCAE NPEGGICQDD SGCTPGKAER KAQGIRTGNC VPFNGTVKTC E IFGWCPVE VDDKIPSPAL LHEAENFTLF IKNSISFPRF KVNRRNLVEE VNGTYMKKCL YHKILHPLCP VFSLGYVVRE SG QDFRSLA EKGGVVGITI DWECDLDWHV RHCKPIYQFH GLYGEKNLSP GFNFRFARHF VQNGTNRRHL FKVFGIRFDI LVD GKAGKF DIIPTMTTIG SGIGIFGVAT VLCDLLLLHI LPKRHYYKQK KFKYAEDMGP GEGERDPAAT SSTLGLQENM RTS

UniProtKB: P2X purinoceptor 1

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 245073
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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