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

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Basic information

Entry
Database: PDB / ID: 5svk
TitleCrystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / Ion Channel / Open 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 / peristalsis / urinary bladder smooth muscle contraction / 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 / peristalsis / urinary bladder smooth muscle contraction / 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 / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / sensory perception of taste / response to heat / postsynapse / receptor complex / response to hypoxia / axon / signal transduction / ATP binding / plasma membrane
Similarity search - Function
P2X3 purinoceptor / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / ADENOSINE-5'-TRIPHOSPHATE / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / P2X purinoceptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.773 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 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_assembly_gen / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_close_contact / 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.occupancy / _atom_site.pdbx_formal_charge / _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_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _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)85,73818
Polymers81,4922
Non-polymers4,24616
Water1,09961
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)129,22430
Polymers122,2383
Non-polymers6,98627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area26190 Å2
ΔGint11 kcal/mol
Surface area49620 Å2
MethodPISA
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)127,99024
Polymers122,2383
Non-polymers5,75221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_577z+1/2,-x+5/2,-y+21
crystal symmetry operation12_774-y+5/2,-z+2,x-1/21
Buried area23150 Å2
ΔGint-24 kcal/mol
Surface area50820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.150, 173.150, 173.150
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-409-

MHA

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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: 40745.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX3 / Production host: Homo sapiens (human) / References: UniProt: P56373

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Sugars , 2 types, 11 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.: 4
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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 , 4 types, 66 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 5.36 Å3/Da / Density % sol: 77.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 400, 50 mM ADA, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 79845 / % possible obs: 99.2 % / Redundancy: 3.94 % / Net I/σ(I): 12.34

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.773→43.287 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 4010 5.02 %
Rwork0.2005 --
obs0.2019 79821 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.773→43.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 273 61 5837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035923
X-RAY DIFFRACTIONf_angle_d0.8928079
X-RAY DIFFRACTIONf_dihedral_angle_d16.8473487
X-RAY DIFFRACTIONf_chiral_restr0.09958
X-RAY DIFFRACTIONf_plane_restr0.004989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7733-2.8060.41861190.38072314X-RAY DIFFRACTION82
2.806-2.84020.34371330.33022559X-RAY DIFFRACTION92
2.8402-2.87610.33221360.30992591X-RAY DIFFRACTION92
2.8761-2.91390.35991380.30842560X-RAY DIFFRACTION92
2.9139-2.95390.33491340.29032524X-RAY DIFFRACTION92
2.9539-2.9960.30731350.28932606X-RAY DIFFRACTION93
2.996-3.04080.32081340.28182586X-RAY DIFFRACTION93
3.0408-3.08830.2911390.27072620X-RAY DIFFRACTION93
3.0883-3.13890.31531350.26172577X-RAY DIFFRACTION93
3.1389-3.1930.24241350.25062606X-RAY DIFFRACTION94
3.193-3.2510.27291410.23482614X-RAY DIFFRACTION94
3.251-3.31350.32751430.23572577X-RAY DIFFRACTION94
3.3135-3.38110.24841420.23462610X-RAY DIFFRACTION94
3.3811-3.45460.24661420.20552668X-RAY DIFFRACTION94
3.4546-3.5350.25021400.21082626X-RAY DIFFRACTION94
3.535-3.62330.25581380.18562626X-RAY DIFFRACTION94
3.6233-3.72120.19581380.19772621X-RAY DIFFRACTION95
3.7212-3.83070.24081380.19772635X-RAY DIFFRACTION95
3.8307-3.95420.22331390.19972659X-RAY DIFFRACTION95
3.9542-4.09550.21561420.18792641X-RAY DIFFRACTION96
4.0955-4.25930.19511380.16942649X-RAY DIFFRACTION96
4.2593-4.4530.15891440.15162705X-RAY DIFFRACTION96
4.453-4.68750.16571400.14832601X-RAY DIFFRACTION95
4.6875-4.98080.18561430.14752687X-RAY DIFFRACTION96
4.9808-5.36470.20551360.15892670X-RAY DIFFRACTION96
5.3647-5.90330.15031400.17072683X-RAY DIFFRACTION97
5.9033-6.75480.22081460.19882693X-RAY DIFFRACTION97
6.7548-8.49970.20691420.19812653X-RAY DIFFRACTION95
8.4997-43.29280.26831400.22282650X-RAY DIFFRACTION95

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