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Yorodumi- PDB-4dw0: Crystal structure of the ATP-gated P2X4 ion channel in the closed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dw0 | |||||||||
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Title | Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 2.9 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: 2.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dw0.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dw0.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/4dw0 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/4dw0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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: 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 Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 84 molecules
#4: Chemical | ChemComp-GD / | ||
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#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.53 Å3/Da / Density % sol: 77.74 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 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: 2.9→50 Å / Num. all: 19275 / Num. obs: 18934 / % possible obs: 98.3 % / Observed criterion σ(I): -1 / Redundancy: 4.6 % |
Reflection shell | Resolution: 2.9→2.95 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 2.9→47.184 Å
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Refine LS restraints |
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LS refinement shell |
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