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- EMDB-66457: ATP-bound structure of P2X332 -

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Basic information

Entry
Database: EMDB / ID: EMD-66457
TitleATP-bound structure of P2X332
Map data
Sample
  • Complex: P2X332 ATP-bound form
    • Protein or peptide: P2X purinoceptor 2
    • Protein or peptide: P2X purinoceptor 3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsP2X / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWang C / Yu Y
Funding support China, 1 items
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, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66457.png

Downloads & links

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Map

FileDownload / File: emd_66457.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å		0.86 Å/pix.
x 300 pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.022513434 - 1.329976
Average (Standard dev.)0.0010198978 (±0.018244034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 256.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66457_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_66457_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 : P2X332 ATP-bound form

EntireName: P2X332 ATP-bound form
Components
  • Complex: P2X332 ATP-bound form
    • Protein or peptide: P2X purinoceptor 2
    • Protein or peptide: P2X purinoceptor 3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: P2X332 ATP-bound form

SupramoleculeName: P2X332 ATP-bound form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: P2X purinoceptor 2

MacromoleculeName: P2X purinoceptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.814996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSE HKVWDVEEYV KPPEGGSVFS IITRVEATHS QTQGTCPESI RVHNATCLSD ADCVAGELDM LGNGLRTGRC V PYYQGPSK ...String:
MAAAQPKYPA GATARRLARG CWSALWDYET PKVIVVRNRR LGVLYRAVQL LILLYFVWYV FIVQKSYQES ETGPESSIIT KVKGITTSE HKVWDVEEYV KPPEGGSVFS IITRVEATHS QTQGTCPESI RVHNATCLSD ADCVAGELDM LGNGLRTGRC V PYYQGPSK TCEVFGWCPV EDGASVSQFL GTMAPNFTIL IKNSIHYPKF HFSKGNIADR TDGYLKRCTF HEASDLYCPI FK LGFIVEK AGESFTELAH KGGVIGVIIN WDCDLDLPAS ECNPKYSFRR LDPKHVPASS GYNFRFAKYY KINGTTTRTL IKA YGIRID VIVHGQAGKF SLIPTIINLA TALTSVGVGS FLCDWILLTF MNKNKVYSHK KFDKVCTPSH PSGSWPVTLA RVLG QAPPE PGHRSEDQHP SPPSGQEGQQ GAECGPAFPP LRPCPISAPS EQMVDTPASE PAQASTPTDP KGLAQL

UniProtKB: P2X purinoceptor 2

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Macromolecule #2: P2X purinoceptor 3

MacromoleculeName: P2X purinoceptor 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.334824 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNCISDFFTY ETTKSVVVKS WTIGIINRVV QLLIISYFVG WVFLHEKAYQ VRDTAIESSV VTKVKGSGLY ANRVMDVSDY VTPPQGTSV FVIITKMIVT ENQMQGFCPE SEEKYRCVSD SQCGPERLPG GGILTGRCVN YSSVLRTCEI QGWCPTEVDT V ETPIMMEA ...String:
MNCISDFFTY ETTKSVVVKS WTIGIINRVV QLLIISYFVG WVFLHEKAYQ VRDTAIESSV VTKVKGSGLY ANRVMDVSDY VTPPQGTSV FVIITKMIVT ENQMQGFCPE SEEKYRCVSD SQCGPERLPG GGILTGRCVN YSSVLRTCEI QGWCPTEVDT V ETPIMMEA ENFTIFIKNS IRFPLFNFEK GNLLPNLTAR DMKTCRFHPD KDPFCPILRV GDVVKFAGQD FAKLARTGGV LG IKIGWVC DLDKAWDQCI PKYSFTRLDS VSEKSSVSPG YNFRFAKYYK MENGSEYRTL LKAFGIRFDV LVYGNAGKFN IIP TIISSV AAFTSVGVGT VLCDIILLNF LKGADQYKAK KFEEVNETTL KIAALTNPVY PSDQTTAEKQ STDSGAFSIG H

UniProtKB: P2X purinoceptor 3

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 6 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 169349
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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