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- PDB-5wzy: Crystal structure of the P2X4 receptor from zebrafish in the pres... -

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Basic information

Entry
Database: PDB / ID: 5wzy
TitleCrystal structure of the P2X4 receptor from zebrafish in the presence of CTP at 2.8 Angstroms
Componentsp2X purinoceptor
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / ATP-gated ion channel activity / CTP binding / monoatomic ion channel complex / response to ATP / monoatomic cation transport ...Elevation of cytosolic Ca2+ levels / Platelet homeostasis / purine nucleotide binding / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / ATP-gated ion channel activity / CTP binding / monoatomic ion channel complex / response to ATP / monoatomic cation transport / ligand-gated monoatomic ion channel activity / transmembrane transporter complex / calcium ion transmembrane transport / calcium ion transport / postsynapse / lysosomal membrane / ATP 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
CYTIDINE-5'-TRIPHOSPHATE / P2X purinoceptor 4a / P2X purinoceptor 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.799 Å
AuthorsKasuya, G. / Hattori, M. / Nureki, O.
Funding support Japan, China, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science24227004 Japan
National Natural Science Foundation of China31650110469 China
National Natural Science Foundation of China31570838 China
Ministry of Science and Technology of China2016YFA0502800 China
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into the nucleotide base specificity of P2X receptors
Authors: Kasuya, G. / Fujiwara, Y. / Tsukamoto, H. / Morinaga, S. / Ryu, S. / Touhara, K. / Ishitani, R. / Furutani, Y. / Hattori, M. / Nureki, O.
History
DepositionJan 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_special_symmetry / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)40,0796
Polymers38,1181
Non-polymers1,9625
Water1,29772
1
A: p2X purinoceptor
hetero molecules

A: p2X purinoceptor
hetero molecules

A: p2X purinoceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,23718
Polymers114,3533
Non-polymers5,88515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area19250 Å2
ΔGint43 kcal/mol
Surface area45100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.242, 129.242, 251.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-670-

HOH

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: p2rx4a / Production host: Spodoptera frugiperda (fall armyworm) / 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, 75 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 5.31 Å3/Da / Density % sol: 76.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3 mM CTP, 20-26% PEG 2000, 300 mM Mg(NO3)2, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 20237 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 67.95 Å2 / Rmerge(I) obs: 0.119 / Χ2: 1.854 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.8-2.855.20.9381.063198.8
2.85-2.960.8421.043199.8
2.9-2.966.60.7841.032199.9
2.96-3.027.10.6671.0861100
3.02-3.087.30.5631.1771100
3.08-3.157.40.5231.1611100
3.15-3.237.60.4271.2071100
3.23-3.327.80.3551.261199.9
3.32-3.427.90.2931.3111100
3.42-3.538.20.2321.424199.9
3.53-3.658.20.1931.4861100
3.65-3.88.40.1581.5571100
3.8-3.978.40.1291.5961100
3.97-4.188.50.1071.7581100
4.18-4.448.70.0862.0281100
4.44-4.798.70.0772.2581100
4.79-5.278.60.0832.9451100
5.27-6.038.40.0883.4361100
6.03-7.598.50.0763.3081100
7.59-508.10.0533.359198.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
HKLdata scaling
RefinementResolution: 2.799→40.101 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.2486 2000 9.89 %
Rwork0.213 --
obs0.2165 20230 99.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 41.932 Å2 / ksol: 0.277 e/Å3
Displacement parametersBiso max: 195.08 Å2 / Biso mean: 78.5943 Å2 / Biso min: 37.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.6797 Å20 Å2-0 Å2
2---5.6797 Å20 Å2
3---11.3593 Å2
Refinement stepCycle: final / Resolution: 2.799→40.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 127 72 2652
Biso mean--85.87 61.99 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092645
X-RAY DIFFRACTIONf_angle_d1.5683613
X-RAY DIFFRACTIONf_chiral_restr0.1427
X-RAY DIFFRACTIONf_plane_restr0.006454
X-RAY DIFFRACTIONf_dihedral_angle_d23.66976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7992-2.86910.43551400.39521281142199
2.8691-2.94670.42051410.341812851426100
2.9467-3.03340.3311390.288112691408100
3.0334-3.13120.29041420.24912911433100
3.1312-3.24310.27181420.230812911433100
3.2431-3.37290.29791410.23112821423100
3.3729-3.52630.24391420.211813071449100
3.5263-3.71210.24791420.200912911433100
3.7121-3.94450.24011420.181112881430100
3.9445-4.24870.18271440.172113111455100
4.2487-4.67570.17721440.137313201464100
4.6757-5.35090.16531440.14713201464100
5.3509-6.73640.25721460.201913231469100
6.7364-40.10560.28991510.27611371152298

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