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- PDB-5svs: Anomalous Mn2+ signal reveals a divalent cation-binding site in t... -

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Basic information

Entry
Database: PDB / ID: 5svs
TitleAnomalous Mn2+ signal reveals a divalent cation-binding site in the head domain of the ATP-gated human P2X3 ion channel
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / Ion Channel / Anomalous Signal Mg ion
Function / homology
Function and homology information


Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / Elevation of cytosolic Ca2+ levels / protein homotrimerization / cellular response to ATP / positive regulation of calcium ion transport into cytosol / positive regulation of calcium-mediated signaling / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission ...Platelet homeostasis / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / Elevation of cytosolic Ca2+ levels / protein homotrimerization / cellular response to ATP / positive regulation of calcium ion transport into cytosol / positive regulation of calcium-mediated signaling / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / calcium ion transmembrane transport / transmembrane transport / signaling receptor complex / postsynapse / axon / signal transduction / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P2X3 purinoceptor / : / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.025 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 23, 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

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Assembly

Deposited unit
A: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7138
Polymers40,7461
Non-polymers9677
Water46826
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)125,13924
Polymers122,2383
Non-polymers2,90221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16080 Å2
ΔGint-14 kcal/mol
Surface area44240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.200, 120.200, 236.240
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

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Protein / Sugars , 2 types, 4 molecules A

#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

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Non-polymers , 5 types, 30 molecules

#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
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 400, 100 mM MES, pH 6.85, 50 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.7712 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 4.03→50 Å / Num. obs: 10534 / % possible obs: 99.7 % / Redundancy: 11.34 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.025→47.775 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 535 5.08 %
Rwork0.2286 --
obs0.2313 10524 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.025→47.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 61 26 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032567
X-RAY DIFFRACTIONf_angle_d0.7863493
X-RAY DIFFRACTIONf_dihedral_angle_d16.6351511
X-RAY DIFFRACTIONf_chiral_restr0.053407
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0252-4.430.30391340.30252477X-RAY DIFFRACTION99
4.43-5.07040.25671340.20012495X-RAY DIFFRACTION100
5.0704-6.38570.27831300.24832518X-RAY DIFFRACTION100
6.3857-47.77880.2731370.21662499X-RAY DIFFRACTION100

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