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- PDB-5svp: Anomalous sulfur signal reveals the position of agonist 2-methylt... -

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Basic information

Entry
Database: PDB / ID: 5svp
TitleAnomalous sulfur signal reveals the position of agonist 2-methylthio-ATP bound to the ATP-gated human P2X3 ion channel in the desensitized state
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / Ion Channel / Desensitized State / 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
Chem-6AT / ADENOSINE-5'-TRIPHOSPHATE / P2X purinoceptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.298 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 / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / 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 1.5Nov 20, 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
B: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,12815
Polymers81,4482
Non-polymers2,68013
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)126,44424
Polymers122,1713
Non-polymers4,27221
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area16360 Å2
ΔGint-20 kcal/mol
Surface area44750 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)125,93921
Polymers122,1713
Non-polymers3,76818
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
Buried area16310 Å2
ΔGint-22 kcal/mol
Surface area43920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.930, 172.930, 172.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein / Sugars , 2 types, 8 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
#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.: 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 , 5 types, 7 molecules

#3: Chemical ChemComp-6AT / 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate) / 2-methylthio-adenosine-5'-triphosphate


Mass: 553.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3S
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

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: 5.34 Å3/Da / Density % sol: 76.97 %
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: 1.5498 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 3.298→50 Å / Num. obs: 50272 / % possible obs: 99.9 % / Redundancy: 5.82 % / Net I/σ(I): 11.75

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.298→47.962 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 2511 5 %
Rwork0.2025 --
obs0.2037 50267 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.298→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 166 0 5094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035221
X-RAY DIFFRACTIONf_angle_d0.7317120
X-RAY DIFFRACTIONf_dihedral_angle_d15.4673067
X-RAY DIFFRACTIONf_chiral_restr0.047819
X-RAY DIFFRACTIONf_plane_restr0.004889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2982-3.36170.37931390.36912583X-RAY DIFFRACTION98
3.3617-3.43030.3491390.30632646X-RAY DIFFRACTION100
3.4303-3.50480.27141430.28252690X-RAY DIFFRACTION100
3.5048-3.58630.2941400.25372638X-RAY DIFFRACTION100
3.5863-3.6760.27561410.24052660X-RAY DIFFRACTION100
3.676-3.77530.24891380.23552659X-RAY DIFFRACTION100
3.7753-3.88640.2791380.22842642X-RAY DIFFRACTION100
3.8864-4.01180.24731410.22222682X-RAY DIFFRACTION100
4.0118-4.15510.22671390.21322663X-RAY DIFFRACTION100
4.1551-4.32130.17571390.16512642X-RAY DIFFRACTION100
4.3213-4.51790.16711390.14482675X-RAY DIFFRACTION100
4.5179-4.75590.1521380.13752631X-RAY DIFFRACTION100
4.7559-5.05350.16371410.14762658X-RAY DIFFRACTION100
5.0535-5.44320.15751380.1542682X-RAY DIFFRACTION100
5.4432-5.99010.21751370.16782642X-RAY DIFFRACTION100
5.9901-6.85470.20051430.19512647X-RAY DIFFRACTION100
6.8547-8.6280.2651380.21112664X-RAY DIFFRACTION100
8.628-47.96720.26971400.24062652X-RAY DIFFRACTION100

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