[English] 日本語
Yorodumi- PDB-5wzy: Crystal structure of the P2X4 receptor from zebrafish in the pres... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wzy | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the P2X4 receptor from zebrafish in the presence of CTP at 2.8 Angstroms | |||||||||||||||
Components | p2X purinoceptor | |||||||||||||||
Keywords | MEMBRANE 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 / transmembrane transporter complex ...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 / transmembrane transporter complex / monoatomic cation transport / ligand-gated monoatomic ion channel activity / calcium ion transmembrane transport / calcium ion transport / postsynapse / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Danio rerio (zebrafish) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.799 Å | |||||||||||||||
Authors | Kasuya, G. / Hattori, M. / Nureki, O. | |||||||||||||||
Funding support | Japan, China, 4items
| |||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wzy.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wzy.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 5wzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wzy ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wzy | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 |
---|
-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 Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 75 molecules
#4: Chemical | #5: Chemical | ChemComp-CTP / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.31 Å3/Da / Density % sol: 76.83 % |
---|---|
Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 17, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.799→40.101 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.07
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 41.932 Å2 / ksol: 0.277 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.08 Å2 / Biso mean: 78.5943 Å2 / Biso min: 37.64 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.799→40.101 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|