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- PDB-5svl: Crystal structure of the ATP-gated human P2X3 ion channel in the ... -

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Basic information

Entry
Database: PDB / ID: 5svl
TitleCrystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, closed (desensitized) state
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / Ion Channel / Desensitized State
Function / homology
Function and homology information


Platelet homeostasis / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / neuromuscular synaptic transmission / Elevation of cytosolic Ca2+ levels / urinary bladder smooth muscle contraction / peristalsis / response to carbohydrate / inorganic cation transmembrane transport / cellular response to ATP ...Platelet homeostasis / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / neuromuscular synaptic transmission / Elevation of cytosolic Ca2+ levels / urinary bladder smooth muscle contraction / peristalsis / response to carbohydrate / inorganic cation transmembrane transport / cellular response to ATP / positive regulation of calcium ion transport into cytosol / behavioral response to pain / protein homotrimerization / positive regulation of calcium-mediated signaling / response to mechanical stimulus / hippocampal mossy fiber to CA3 synapse / response to cold / establishment of localization in cell / calcium ion transmembrane transport / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / sensory perception of taste / response to heat / postsynapse / response to hypoxia / receptor complex / axon / signal transduction / ATP 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 receptor / ATP P2X receptors signature. / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich ...P2X3 purinoceptor / atp-gated p2x4 ion channel / atp-gated p2x4 ion channel fold / atp-gated p2x4 ion channel domain / ATP P2X receptor / ATP P2X receptors signature. / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / P2X purinoceptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMansoor, S.E. / Lu, W. / Oosterheert, W. / Shekhar, M. / Tajkhorshid, E. / Gouaux, E.
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 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P2X purinoceptor 3
B: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,87224
Polymers81,4482
Non-polymers3,42522
Water1,65792
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)128,31445
Polymers122,1713
Non-polymers6,14342
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: P2X purinoceptor 3
hetero molecules

B: P2X purinoceptor 3
hetero molecules

B: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,30227
Polymers122,1713
Non-polymers4,13124
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Unit cell
Length a, b, c (Å)172.140, 172.140, 172.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-414-

TRS

21A-414-

TRS

31B-544-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40723.828 Da / Num. of mol.: 2
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

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Sugars , 2 types, 7 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 107 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 5.27 Å3/Da / Density % sol: 76.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 400, 100 mM Tris, pH 8.0, 325 mM Sodium Acetate, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→80 Å / Num. obs: 62472 / % possible obs: 97.6 % / Redundancy: 2.84 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
PHENIXdev_1634refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→76.983 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 3118 4.99 %
Rwork0.2052 --
obs0.2069 62465 85.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→76.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 216 92 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065342
X-RAY DIFFRACTIONf_angle_d1.357251
X-RAY DIFFRACTIONf_dihedral_angle_d16.8751901
X-RAY DIFFRACTIONf_chiral_restr0.061846
X-RAY DIFFRACTIONf_plane_restr0.006901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-2.94550.35451380.35092680X-RAY DIFFRACTION85
2.9455-2.99380.33161410.33142633X-RAY DIFFRACTION85
2.9938-3.04540.33611380.31262708X-RAY DIFFRACTION85
3.0454-3.10080.30061350.29552668X-RAY DIFFRACTION85
3.1008-3.16040.33881430.28092659X-RAY DIFFRACTION85
3.1604-3.2250.31561470.28032698X-RAY DIFFRACTION85
3.225-3.29510.33361420.27612700X-RAY DIFFRACTION86
3.2951-3.37170.28221410.24452672X-RAY DIFFRACTION84
3.3717-3.4560.27651210.22242433X-RAY DIFFRACTION76
3.456-3.54950.25831370.20612644X-RAY DIFFRACTION85
3.5495-3.65390.24761400.19752742X-RAY DIFFRACTION87
3.6539-3.77190.24651440.19812769X-RAY DIFFRACTION87
3.7719-3.90670.23741480.19982772X-RAY DIFFRACTION88
3.9067-4.06310.23831490.18892762X-RAY DIFFRACTION88
4.0631-4.2480.21991410.1762707X-RAY DIFFRACTION87
4.248-4.47190.19051440.14732641X-RAY DIFFRACTION84
4.4719-4.75210.20311430.14072681X-RAY DIFFRACTION84
4.7521-5.11890.17911530.15072795X-RAY DIFFRACTION89
5.1189-5.63390.16051540.15742792X-RAY DIFFRACTION88
5.6339-6.44880.22431460.19012749X-RAY DIFFRACTION87
6.4488-8.12340.25041340.22252694X-RAY DIFFRACTION85
8.1234-77.01040.26541390.2462748X-RAY DIFFRACTION87

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