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- EMDB-60445: Structure of calcium preference ATP-gated channel Apo-P2X1 in the... -

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Basic information

Entry
Database: EMDB / ID: EMD-60445
TitleStructure of calcium preference ATP-gated channel Apo-P2X1 in the Desensitized state 1
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 / regulation of vascular associated smooth muscle contraction / insemination / positive regulation of monoatomic ion transport / positive regulation of calcium ion import across plasma membrane / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / suramin binding / serotonin secretion by platelet ...Platelet homeostasis / Elevation of cytosolic Ca2+ levels / regulation of vascular associated smooth muscle contraction / insemination / positive regulation of monoatomic ion transport / positive regulation of calcium ion import across plasma membrane / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / suramin binding / serotonin secretion by platelet / ligand-gated calcium channel activity / regulation of presynaptic cytosolic calcium ion concentration / regulation of smooth muscle contraction / ceramide biosynthetic process / response to ATP / regulation of synaptic vesicle exocytosis / regulation of calcium ion transport / regulation of vasoconstriction / neuronal action potential / monoatomic cation channel activity / monoatomic ion transport / presynaptic active zone membrane / Neutrophil degranulation / synaptic transmission, glutamatergic / establishment of localization in cell / platelet activation / regulation of blood pressure / postsynaptic membrane / membrane raft / external side of plasma membrane / apoptotic process / protein-containing complex binding / glutamatergic synapse / protein-containing complex / ATP binding / identical protein binding
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: 2.31 Å
AuthorsZhang H / Xu HE
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of ion permeation, calcium selectivity, and pore blocking at the P2X1 receptor
Authors: Zhang H / Xu HE
History
DepositionJun 6, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60445.png

Downloads & links

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Map

FileDownload / File: emd_60445.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.7106297 - 2.1112936
Average (Standard dev.)0.00075663516 (±0.051953323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60445_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60445_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 48.54466 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMARRLQDEL SAFFFEYDTP RMVLVRNKKV GVIFRLIQLV VLVYVIGWVF VYEKGYQTSS GLISSVSVKL KGLAVTQLQG LGPQVWDVA DYVFPAHGDS SFVVMTNFIM TPQQAQGHCA ENPEGGICQD DSGCTPGKAE RKAQGIRTGN CVPFNGTVKT C EIFGWCPV ...String:
MMARRLQDEL SAFFFEYDTP RMVLVRNKKV GVIFRLIQLV VLVYVIGWVF VYEKGYQTSS GLISSVSVKL KGLAVTQLQG LGPQVWDVA DYVFPAHGDS SFVVMTNFIM TPQQAQGHCA ENPEGGICQD DSGCTPGKAE RKAQGIRTGN CVPFNGTVKT C EIFGWCPV EVDDKIPSPA LLHEAENFTL FIKNSISFPR FKVNRRNLVE EVNGTYMKKC LYHKILHPLC PVFSLGYVVR ES GQDFRSL AEKGGVVGIT IDWECDLDWH VRHCKPIYQF HGLYGEKNLS PGFNFRFARH FVQNGTNRRH LFKVFGIRFD ILV DGKAGK FDIIPTMTTI GSGIGIFGVA TVLCDLLLLH ILPKRHYYKQ KKFKYAEDMG PGEGERDPAA TSSTLGLQEN MRTS KLLEV LFQGPHHHHH HHHHHDYKDD DDK

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: 1 / 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

MicroscopeFEI POLARA 300
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: Tecnai Polara / 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: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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