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- PDB-4dw1: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bo... -

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Basic information

Entry
Database: PDB / ID: 4dw1
TitleCrystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms
ComponentsP2X purinoceptor
KeywordsTRANSPORT PROTEIN / ion channel
Function / homology
Function and homology information


Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / transmembrane transporter complex / ATP-gated ion channel activity / ligand-gated monoatomic ion channel activity / CTP binding / response to ATP ...Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / transmembrane transporter complex / ATP-gated ion channel activity / ligand-gated monoatomic ion channel activity / CTP binding / response to ATP / monoatomic cation transport / monoatomic ion channel complex / calcium ion transport / postsynapse / lysosomal membrane / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
P2X4 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 ...P2X4 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
ADENOSINE-5'-TRIPHOSPHATE / P2X purinoceptor 4a / P2X purinoceptor 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHattori, M. / Gouaux, E.
CitationJournal: Nature / Year: 2012
Title: Molecular mechanism of ATP binding and ion channel activation in P2X receptors.
Authors: Hattori, M. / Gouaux, E.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1036
Polymers38,1181
Non-polymers1,9865
Water1,65792
1
A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,30918
Polymers114,3533
Non-polymers5,95715
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 area19650 Å2
ΔGint54 kcal/mol
Surface area44500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.791, 128.791, 252.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer generated from the protomer in the asymmetric unit by the operations: -y, x-y, z and y-x, -x, z.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein P2X purinoceptor


Mass: 38117.625 Da / Num. of mol.: 1 / Fragment: UNP residues 28-365 / Mutation: N78K, N187R, H252R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: p2rx4a / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q6NYR1, UniProt: F8W463*PLUS

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 1
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, 95 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 5

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Sample preparation

CrystalDensity Matthews: 5.28 Å3/Da / Density % sol: 76.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 mM ATP, 20-26% PEG 2000, 300 mM Mg(NO3)2, 100 mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2011
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 20144 / Num. obs: 19941 / % possible obs: 99 % / Observed criterion σ(I): -1 / Redundancy: 7.8 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.94 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 1015 5.09 %
Rwork0.2081 --
obs0.2104 19928 98.97 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.039 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8523 Å2-0 Å2-0 Å2
2---6.8523 Å20 Å2
3---13.7045 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 129 92 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132718
X-RAY DIFFRACTIONf_angle_d1.5663612
X-RAY DIFFRACTIONf_dihedral_angle_d23.591971
X-RAY DIFFRACTIONf_chiral_restr0.098427
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.30051420.26842649X-RAY DIFFRACTION99
2.9476-3.13230.26591540.21242671X-RAY DIFFRACTION99
3.1323-3.3740.20121620.19212662X-RAY DIFFRACTION100
3.374-3.71340.22281400.16382714X-RAY DIFFRACTION100
3.7134-4.25040.24461230.17272715X-RAY DIFFRACTION99
4.2504-5.35380.2251580.17652723X-RAY DIFFRACTION99
5.3538-45.9460.30431360.26182779X-RAY DIFFRACTION97

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