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- PDB-9xqr: Cryo-EM structure of P1X1 in complex with BTFA -

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Basic information

Entry
Database: PDB / ID: 9xqr
TitleCryo-EM structure of P1X1 in complex with BTFA
ComponentsP2X purinoceptor 1
KeywordsMEMBRANE 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 / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / suramin binding / serotonin secretion by platelet / regulation of vascular associated smooth muscle contraction ...Platelet homeostasis / Elevation of cytosolic Ca2+ levels / 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 / regulation of vascular associated smooth muscle contraction / regulation of presynaptic cytosolic calcium ion concentration / ligand-gated calcium channel activity / regulation of smooth muscle contraction / ceramide biosynthetic process / response to ATP / regulation of synaptic vesicle exocytosis / monoatomic cation transmembrane transport / regulation of calcium ion transport / regulation of vasoconstriction / neuronal action potential / monoatomic cation channel activity / monoatomic ion transport / Neutrophil degranulation / presynaptic active zone membrane / synaptic transmission, glutamatergic / platelet activation / calcium ion transmembrane transport / regulation of blood pressure / 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: 3.14 Å
AuthorsZhang, H.
Funding support China, 1items
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.
History
DepositionNov 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,76814
Polymers145,2403
Non-polymers2,52711
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein / Sugars , 2 types, 6 molecules BCA

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


Mass: 48413.465 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
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 , 5 types, 11 molecules

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


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-A1D8Z / 3,5-bis(trifluoromethyl)aniline / 3,5-Di(trifluoromethyl)aniline


Mass: 229.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F6N / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: mouse P2X purinoceptor 1 / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
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 software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218684 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028237
ELECTRON MICROSCOPYf_angle_d0.50911183
ELECTRON MICROSCOPYf_dihedral_angle_d16.0312969
ELECTRON MICROSCOPYf_chiral_restr0.0441238
ELECTRON MICROSCOPYf_plane_restr0.0041406

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