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- EMDB-64572: Cryo-EM structure of the human P2X3 receptor in the camlipixant-b... -

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Basic information

Entry
Database: EMDB / ID: EMD-64572
TitleCryo-EM structure of the human P2X3 receptor in the camlipixant-bound inhibited state
Map data
Sample
  • Complex: P2X purinoceptor 3
    • Protein or peptide: P2X purinoceptor 3
  • Ligand: Camlipixant
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsP2X ion channal / MEMBRANE PROTEIN
Function / homology
Function and homology information


Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / peristalsis / Elevation of cytosolic Ca2+ levels / neuromuscular synaptic transmission / urinary bladder smooth muscle contraction / response to carbohydrate / : / protein homotrimerization ...Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / peristalsis / Elevation of cytosolic Ca2+ levels / neuromuscular synaptic transmission / urinary bladder smooth muscle contraction / response to carbohydrate / : / protein homotrimerization / cellular response to ATP / behavioral response to pain / positive regulation of calcium ion transport into cytosol / response to mechanical stimulus / positive regulation of calcium-mediated signaling / establishment of localization in cell / response to cold / hippocampal mossy fiber to CA3 synapse / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / calcium ion transmembrane transport / sensory perception of taste / response to heat / response to hypoxia / signaling receptor complex / postsynapse / axon / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P2X3 purinoceptor / : / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsZhang J / Cheng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the human P2X3 receptor in the camlipixant-bound inhibited state
Authors: Zhang J / Cheng XY
History
DepositionMay 13, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64572.png

Downloads & links

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Map

FileDownload / File: emd_64572.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.4482548 - 1.483224
Average (Standard dev.)-0.0009810153 (±0.027094882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64572_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_64572_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 : P2X purinoceptor 3

EntireName: P2X purinoceptor 3
Components
  • Complex: P2X purinoceptor 3
    • Protein or peptide: P2X purinoceptor 3
  • Ligand: Camlipixant
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: P2X purinoceptor 3

SupramoleculeName: P2X purinoceptor 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: P2X purinoceptor 3

MacromoleculeName: P2X purinoceptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.73241 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SWTIGIINRV VQLLIISYFV GWVFLHEKAY QVRDTAIESS VVTKVKGSGL YANRVMDVSD YVTPPQGTSV FVIITKMIVT ENQMQGFCP ESEEKYRCVS DSQCGPERLP GGGILTGRCV NYSSVLRTCE IQGWCPTEVD TVETPIMMEA ENFTIFIKNS I RFPLFNFE ...String:
SWTIGIINRV VQLLIISYFV GWVFLHEKAY QVRDTAIESS VVTKVKGSGL YANRVMDVSD YVTPPQGTSV FVIITKMIVT ENQMQGFCP ESEEKYRCVS DSQCGPERLP GGGILTGRCV NYSSVLRTCE IQGWCPTEVD TVETPIMMEA ENFTIFIKNS I RFPLFNFE KGNLLPNLTA RDMKTCRFHP DKDPFCPILR VGDVVKFAGQ DFAKLARTGG VLGIKIGWVC DLDKAWDQCI PK YSFTRLD SVSEKSSVSP GYNFRFAKYY KMENGSEYRT LLKAFGIRFD VLVYGNAGKF NIIPTIISSV AAFTSVGVGT VLC DIILLN FL

UniProtKB: P2X purinoceptor 3

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Macromolecule #2: Camlipixant

MacromoleculeName: Camlipixant / type: ligand / ID: 2 / Number of copies: 3 / Formula: A1AQX
Molecular weightTheoretical: 458.458 Da

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / 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: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158665
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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