[English] 日本語
Yorodumi- PDB-4dw1: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dw1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms | |||||||||
Components | P2X purinoceptor | |||||||||
Keywords | TRANSPORT PROTEIN / ion channel | |||||||||
Function / homology | Function and homology information purine nucleotide binding / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / ATP-gated ion channel activity / transmembrane transporter complex / CTP binding / monoatomic ion channel complex / response to ATP / ligand-gated monoatomic ion channel activity / monoatomic cation transport ...purine nucleotide binding / purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / ATP-gated ion channel activity / transmembrane transporter complex / CTP binding / monoatomic ion channel complex / response to ATP / ligand-gated monoatomic ion channel activity / monoatomic cation transport / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Hattori, M. / Gouaux, E. | |||||||||
Citation | Journal: Nature / Year: 2012 Title: Molecular mechanism of ATP binding and ion channel activation in P2X receptors. Authors: Hattori, M. / Gouaux, E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dw1.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dw1.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/4dw1 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/4dw1 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The 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. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 |
---|
-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, 95 molecules
#4: Chemical | ChemComp-ATP / | ||
---|---|---|---|
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
---|
-Sample preparation
Crystal | Density Matthews: 5.28 Å3/Da / Density % sol: 76.69 % |
---|---|
Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2011 |
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 20144 / Num. obs: 19941 / % possible obs: 99 % / Observed criterion σ(I): -1 / Redundancy: 7.8 % |
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage 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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|