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Yorodumi- PDB-4xdj: Crystal structure of human two pore domain potassium ion channel ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xdj | ||||||
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Title | Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in an alternate conformation (FORM 2) | ||||||
Components | POTASSIUM CHANNEL SUBFAMILY K MEMBER 10 | ||||||
Keywords | TRANSPORT PROTEIN / OUTWARD RECTIFICATION / MEMBRANE PROTEIN / K2P / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / memory / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Pike, A.C.W. / Dong, Y.Y. / Mackenzie, A. / Mukhopadhyay, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Science / Year: 2015 Title: K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac. Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, ...Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, P.E. / Burgess-Brown, N.A. / Sansom, M.S. / Tucker, S.J. / Carpenter, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xdj.cif.gz | 378 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xdj.ent.gz | 308 KB | Display | PDB format |
PDBx/mmJSON format | 4xdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xdj ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xdj | HTTPS FTP |
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-Related structure data
Related structure data | 4bw5SC 4xdkC 4xdlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31060.111 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 67-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) homo sapiens (human) / Plasmid: PFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P57789 #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PC1 / #4: Chemical | ChemComp-TRD / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M KCl, 0.1M sodium cacodylate pH6.5, 22% (w/v) PEG1500 + 3% (v/v) Methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→38.37 Å / Num. obs: 18910 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 129.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BW5 Resolution: 3.8→37.26 Å / Cor.coef. Fo:Fc: 0.8426 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.614
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Displacement parameters | Biso mean: 164.38 Å2
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Refine analyze | Luzzati coordinate error obs: 1.129 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.8→37.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→4.03 Å / Total num. of bins used: 9
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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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