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- PDB-4dw0: Crystal structure of the ATP-gated P2X4 ion channel in the closed... -

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Basic information

Entry
Database: PDB / ID: 4dw0
TitleCrystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 2.9 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
GADOLINIUM ATOM / P2X purinoceptor 4a / P2X purinoceptor 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Atomic model / Data collection ...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_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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.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 2.1Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6578
Polymers38,1621
Non-polymers1,4967
Water1,42379
1
A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules

A: P2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,97224
Polymers114,4853
Non-polymers4,48721
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area19690 Å2
ΔGint22 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.626, 99.626, 441.539
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-506-

GD

21A-626-

HOH

31A-627-

HOH

41A-650-

HOH

51A-655-

HOH

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: 38161.656 Da / Num. of mol.: 1 / Fragment: UNP residues 28-381 / Mutation: C51F, 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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+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, 84 molecules

#4: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 5.53 Å3/Da / Density % sol: 77.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 mM GdCl3, 20% PEG 3350, 100 mM MgCl2, 2M NaCl and 100 mM imidazole, pH 6.5, 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 10, 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: 2.9→50 Å / Num. all: 19275 / Num. obs: 18934 / % possible obs: 98.3 % / Observed criterion σ(I): -1 / Redundancy: 4.6 %
Reflection shellResolution: 2.9→2.95 Å / % possible all: 98.8

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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: 2.9→47.184 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 27.41 / Stereochemistry target values: ML
Details: AUTHORS STATED THAT EVEN THOUGH THERE IS AN APPARENT GAP IN THE LATTICE, AUTHORS KNOW THAT THERE ARE STILL MANY AMINO ACID RESIDUES THAT AUTHORS HAVE NOT BEEN ABLE TO MODEL IN THE STRUCTURE ...Details: AUTHORS STATED THAT EVEN THOUGH THERE IS AN APPARENT GAP IN THE LATTICE, AUTHORS KNOW THAT THERE ARE STILL MANY AMINO ACID RESIDUES THAT AUTHORS HAVE NOT BEEN ABLE TO MODEL IN THE STRUCTURE AND WE BELIEVE THAT THESE RESIDUES ARE WHAT PROVIDE THE INTERACTIONS BETWEEN THE LAYERS
RfactorNum. reflection% reflection
Rfree0.2442 968 5.12 %
Rwork0.2196 --
obs0.2209 18911 97.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--25.6468 Å2-0 Å20 Å2
2---25.6468 Å20 Å2
3---51.2935 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 89 79 2670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112735
X-RAY DIFFRACTIONf_angle_d1.3853608
X-RAY DIFFRACTIONf_dihedral_angle_d19.362962
X-RAY DIFFRACTIONf_chiral_restr0.093417
X-RAY DIFFRACTIONf_plane_restr0.006462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8921-3.04460.30561150.31942370X-RAY DIFFRACTION91
3.0446-3.23530.29721550.24912536X-RAY DIFFRACTION99
3.2353-3.4850.19421480.20312578X-RAY DIFFRACTION99
3.485-3.83560.22091350.18062592X-RAY DIFFRACTION99
3.8356-4.39030.24311330.1922598X-RAY DIFFRACTION99
4.3903-5.52990.221410.17762600X-RAY DIFFRACTION98
5.5299-47.19010.27031410.26512669X-RAY DIFFRACTION96

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