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- PDB-5yve: Crystal structure of human P2X3 receptor in complex with the AF-2... -

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Basic information

Entry
Database: PDB / ID: 5yve
TitleCrystal structure of human P2X3 receptor in complex with the AF-219 negative allosteric modulator
ComponentsP2X purinoceptor 3
KeywordsTRANSPORT PROTEIN / ion channels / ATP
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
Chem-AF9 / P2X purinoceptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWang, Y. / Hattori, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Druggable negative allosteric site of P2X3 receptors.
Authors: Wang, J. / Wang, Y. / Cui, W.W. / Huang, Y. / Yang, Y. / Liu, Y. / Zhao, W.S. / Cheng, X.Y. / Sun, W.S. / Cao, P. / Zhu, M.X. / Wang, R. / Hattori, M. / Yu, Y.
History
DepositionNov 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7376
Polymers40,8941
Non-polymers8435
Water0
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)125,21218
Polymers122,6823
Non-polymers2,52915
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 area15010 Å2
ΔGint-164 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.613, 119.613, 235.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 40894.078 Da / Num. of mol.: 1 / Mutation: T13P,S15V,V16I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RX3 / Production host: Homo sapiens (human) / References: UniProt: P56373
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 2 / 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
#5: Chemical ChemComp-AF9 / 5-[2,4-bis(azanyl)pyrimidin-5-yl]oxy-2-methoxy-4-propan-2-yl-benzenesulfonamide / AF-219


Mass: 353.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N5O4S

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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: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.05M MgCl2, 0.1M Glycine pH 9.0, 22-24% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 17203 / % possible obs: 99.5 % / Redundancy: 4.9 % / Net I/σ(I): 14.45
Reflection shellResolution: 3.4→3.6 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→47.587 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.07
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2956 1719 9.99 %
Rwork0.2353 --
obs0.2405 17203 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→47.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 54 0 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052597
X-RAY DIFFRACTIONf_angle_d0.9033544
X-RAY DIFFRACTIONf_dihedral_angle_d17.5561523
X-RAY DIFFRACTIONf_chiral_restr0.048407
X-RAY DIFFRACTIONf_plane_restr0.004449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.50020.28961450.31411288X-RAY DIFFRACTION98
3.5002-3.61310.31711450.31861298X-RAY DIFFRACTION100
3.6131-3.74220.31461450.31291289X-RAY DIFFRACTION100
3.7422-3.89190.33141410.27921303X-RAY DIFFRACTION100
3.8919-4.0690.31821400.25311281X-RAY DIFFRACTION99
4.069-4.28340.25891420.21851275X-RAY DIFFRACTION99
4.2834-4.55160.22321460.19761299X-RAY DIFFRACTION100
4.5516-4.90270.23231400.18411281X-RAY DIFFRACTION99
4.9027-5.39540.27061440.18481295X-RAY DIFFRACTION99
5.3954-6.17470.2491410.21361295X-RAY DIFFRACTION99
6.1747-7.7740.29551460.261283X-RAY DIFFRACTION99
7.774-47.59170.35381440.24381297X-RAY DIFFRACTION99

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