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- PDB-6ah4: Structure of human P2X3 receptor in complex with ATP and Ca2+ ion -

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Basic information

Entry
Database: PDB / ID: 6ah4
TitleStructure of human P2X3 receptor in complex with ATP and Ca2+ ion
ComponentsP2X purinoceptor 3
KeywordsMEMBRANE PROTEIN / channel
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 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 / P2X purinoceptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.296 Å
AuthorsHattori, M.
CitationJournal: Elife / Year: 2019
Title: Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP.
Authors: Li, M. / Wang, Y. / Banerjee, R. / Marinelli, F. / Silberberg, S. / Faraldo-Gomez, J.D. / Hattori, M. / Swartz, K.J.
History
DepositionAug 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 23, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
C: P2X purinoceptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,03026
Polymers122,3793
Non-polymers5,65123
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-47 kcal/mol
Surface area50920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.903, 142.500, 325.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 40792.977 Da / Num. of mol.: 3 / Fragment: UNP residues 17-363
Source method: isolated from a genetically manipulated source
Details: ATP is a ligand. / 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, 14 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.: 6
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-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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 , 3 types, 9 molecules

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


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: 5.1 Å3/Da / Density % sol: 75.87 %
Crystal growTemperature: 297 K / Method: vapor diffusion / Details: Sodium chloride, Calcium acetate, PEG 400, ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.296→50 Å / Num. obs: 75110 / % possible obs: 99.9 % / Redundancy: 7.2 % / Net I/σ(I): 12.77
Reflection shellResolution: 3.3→3.5 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.296→48.047 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.76
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2898 3818 5.1 %
Rwork0.2404 --
obs0.2428 74823 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.296→48.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8556 0 112 0 8668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018890
X-RAY DIFFRACTIONf_angle_d1.41612107
X-RAY DIFFRACTIONf_dihedral_angle_d11.8295208
X-RAY DIFFRACTIONf_chiral_restr0.0751429
X-RAY DIFFRACTIONf_plane_restr0.0091483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2961-3.33780.55881410.50642604X-RAY DIFFRACTION97
3.3378-3.38170.47131390.43312585X-RAY DIFFRACTION100
3.3817-3.4280.43431360.40942581X-RAY DIFFRACTION99
3.428-3.4770.43311510.38282722X-RAY DIFFRACTION99
3.477-3.52880.44691360.37242521X-RAY DIFFRACTION100
3.5288-3.5840.43761410.34362662X-RAY DIFFRACTION99
3.584-3.64270.40391390.33832637X-RAY DIFFRACTION100
3.6427-3.70550.34841400.35082612X-RAY DIFFRACTION99
3.7055-3.77290.45421430.32782650X-RAY DIFFRACTION99
3.7729-3.84540.31341380.28572608X-RAY DIFFRACTION99
3.8454-3.92380.27311480.25182697X-RAY DIFFRACTION100
3.9238-4.00910.25761400.2322528X-RAY DIFFRACTION99
4.0091-4.10230.30671440.21132707X-RAY DIFFRACTION100
4.1023-4.20490.27821370.2072562X-RAY DIFFRACTION100
4.2049-4.31850.19591430.19112706X-RAY DIFFRACTION100
4.3185-4.44550.22411400.17852601X-RAY DIFFRACTION100
4.4455-4.58890.2331430.17752613X-RAY DIFFRACTION100
4.5889-4.75270.21841470.17252694X-RAY DIFFRACTION100
4.7527-4.94280.24341320.1622578X-RAY DIFFRACTION100
4.9428-5.16750.23071460.16392655X-RAY DIFFRACTION100
5.1675-5.43960.23811370.17722631X-RAY DIFFRACTION100
5.4396-5.77990.25271440.19132643X-RAY DIFFRACTION100
5.7799-6.22530.26921410.20232650X-RAY DIFFRACTION100
6.2253-6.85020.28041380.21592646X-RAY DIFFRACTION100
6.8502-7.83770.29721470.22912652X-RAY DIFFRACTION100
7.8377-9.86070.22191400.20962630X-RAY DIFFRACTION100
9.8607-48.05190.33351470.29252630X-RAY DIFFRACTION99

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