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- PDB-4dw0: Crystal structure of the ATP-gated P2X4 ion channel in the closed... -
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Open data
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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 | |||||||||
![]() | P2X purinoceptor | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hattori, M. / Gouaux, E. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#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 ![](data/chem/img/GD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GD / | ||
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#5: Chemical | ChemComp-GOL / ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine 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 ...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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