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- PDB-6rv3: Crystal structure of the human two pore domain potassium ion chan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rv3 | ||||||||||||
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Title | Crystal structure of the human two pore domain potassium ion channel TASK-1 (K2P3.1) in a closed conformation with a bound inhibitor BAY 1000493 | ||||||||||||
![]() | Potassium channel subfamily K member 3 | ||||||||||||
![]() | MEMBRANE PROTEIN / potassium channel / Structural Genomics / Structural Genomics Consortium / SGC | ||||||||||||
Function / homology | ![]() open rectifier potassium channel activity / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / regulation of resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / S100 protein binding / cellular response to zinc ion / cochlea development ...open rectifier potassium channel activity / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / regulation of resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / S100 protein binding / cellular response to zinc ion / cochlea development / negative regulation of cytosolic calcium ion concentration / potassium channel activity / monoatomic ion transmembrane transport / potassium ion transmembrane transport / potassium ion transport / monoatomic ion channel activity / cellular response to hypoxia / chemical synaptic transmission / response to xenobiotic stimulus / synapse / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. ...Rodstrom, K.E.J. / Pike, A.C.W. / Zhang, W. / Quigley, A. / Speedman, D. / Mukhopadhyay, S.M.M. / Shrestha, L. / Chalk, R. / Venkaya, S. / Bushell, S.R. / Tessitore, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A lower X-gate in TASK channels traps inhibitors within the vestibule. Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / ...Authors: Rodstrom, K.E.J. / Kiper, A.K. / Zhang, W. / Rinne, S. / Pike, A.C.W. / Goldstein, M. / Conrad, L.J. / Delbeck, M. / Hahn, M.G. / Meier, H. / Platzk, M. / Quigley, A. / Speedman, D. / Shrestha, L. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / Tucker, S.J. / Muller, T. / Decher, N. / Carpenter, E.P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.2 KB | Display | ![]() |
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PDB format | ![]() | 354.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rv2C ![]() 6rv4C ![]() 4bw5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/DMU.gif)
![](data/chem/img/DMU.gif)
#1: Protein | Mass: 30117.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Two-pore domain potassium channel K2P3.1 (TASK-1) / Source: (gene. exp.) ![]() ![]() ![]() #4: Sugar | ChemComp-DMU / |
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-Non-polymers , 5 types, 51 molecules ![](data/chem/img/K.gif)
![](data/chem/img/Y01.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/KKQ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/Y01.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/KKQ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-Y01 / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS pH 8.5, 0.05 M KCl, 24% v/v PEG 400, 3% w/v sucrose Temp details: Ambient |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→44.291 Å / Num. obs: 40478 / % possible obs: 80 % / Redundancy: 3.9 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.094 / Rrim(I) all: 0.194 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.9→3.005 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2024 / CC1/2: 0.795 / Rpim(I) all: 0.421 / Rrim(I) all: 0.86 / % possible all: 40 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BW5 Resolution: 2.9→41.31 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.865 / SU R Cruickshank DPI: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.851 / SU Rfree Blow DPI: 0.341 / SU Rfree Cruickshank DPI: 0.348 Details: Refined against STARANISO anisotropically truncated data
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Displacement parameters | Biso mean: 48.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→41.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.94 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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