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- PDB-5svt: Anomalous Cs+ signal reveals the site of Na+ ion entry to the cha... -

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Basic information

Entry
Database: PDB / ID: 5svt
TitleAnomalous Cs+ signal reveals the site of Na+ ion entry to the channel pore of the human P2X3 ion channel through the extracellular fenestrations
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / Ion Channel / Anomalous Signal
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 / response to cold / hippocampal mossy fiber to CA3 synapse / establishment of localization in cell / regulation of synaptic plasticity / calcium ion transmembrane transport / Schaffer collateral - CA1 synapse / sensory perception of taste / response to heat / response to hypoxia / receptor complex / postsynapse / axon / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P2X3 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins ...P2X3 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.794 Å
AuthorsMansoor, S.E. / Lu, W. / Oosterheert, W. / Shekhar, M. / Tajkhorshid, E. / Gouaux, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5F32GM108391 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100400 United States
CitationJournal: Nature / Year: 2016
Title: X-ray structures define human P2X3 receptor gating cycle and antagonist action.
Authors: Mansoor, S.E. / Lu, W. / Oosterheert, W. / Shekhar, M. / Tajkhorshid, E. / Gouaux, E.
History
DepositionAug 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4576
Polymers40,7461
Non-polymers7115
Water00
1
A: P2X purinoceptor 3
hetero molecules

A: P2X purinoceptor 3
hetero molecules

A: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,37118
Polymers122,2383
Non-polymers2,13315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16910 Å2
ΔGint-62 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.950, 119.950, 236.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-405-

NA

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Components

#1: Protein P2X purinoceptor 3 / P2X3 / ATP receptor / Purinergic receptor


Mass: 40745.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P56373
#2: 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: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 400, 100 mM MES, pH 6.85, 50 mM MgCl2, 100 mM CsCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.9074 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9074 Å / Relative weight: 1
ReflectionResolution: 3.79→50 Å / Num. obs: 12566 / % possible obs: 99.8 % / Redundancy: 7.8 % / Net I/σ(I): 13.42

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.794→47.725 Å / SU ML: 1.02 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 49.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3119 627 5 %
Rwork0.2763 --
obs0.278 12536 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.794→47.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 44 0 2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032541
X-RAY DIFFRACTIONf_angle_d0.7693466
X-RAY DIFFRACTIONf_dihedral_angle_d16.4311495
X-RAY DIFFRACTIONf_chiral_restr0.113406
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7943-4.17590.57781570.512973X-RAY DIFFRACTION99
4.1759-4.77970.3361580.29182971X-RAY DIFFRACTION100
4.7797-6.020.29821530.26552977X-RAY DIFFRACTION100
6.02-47.72890.29171590.25762988X-RAY DIFFRACTION100

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