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Yorodumi- PDB-3ukm: Crystal structure of the human two pore domain potassium ion chan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ukm | ||||||
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Title | Crystal structure of the human two pore domain potassium ion channel K2P1 (TWIK-1) | ||||||
Components | Potassium channel subfamily K member 1 | ||||||
Keywords | MEMBRANE PROTEIN / potassium channel / eukaryotic / two-pore domain potassium channel / K2P channel / membrane | ||||||
Function / homology | Function and homology information Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / inward rectifier potassium channel complex / Phase 4 - resting membrane potential / potassium channel complex / stabilization of membrane potential / regulation of resting membrane potential / potassium ion leak channel activity / cardiac conduction / inward rectifier potassium channel activity / sodium channel activity ...Tandem of pore domain in a weak inwardly rectifying K+ channels (TWIK) / inward rectifier potassium channel complex / Phase 4 - resting membrane potential / potassium channel complex / stabilization of membrane potential / regulation of resting membrane potential / potassium ion leak channel activity / cardiac conduction / inward rectifier potassium channel activity / sodium channel activity / plasma membrane => GO:0005886 / potassium channel activity / sodium ion transmembrane transport / voltage-gated potassium channel complex / potassium ion transmembrane transport / potassium ion transport / synaptic membrane / brush border membrane / response to nicotine / recycling endosome / perikaryon / membrane => GO:0016020 / apical plasma membrane / intracellular membrane-bounded organelle / dendrite / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.4 Å | ||||||
Authors | Long, S.B. / Miller, A.N. | ||||||
Citation | Journal: Science / Year: 2012 Title: Crystal structure of the human two-pore domain potassium channel K2P1. Authors: Miller, A.N. / Long, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ukm.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ukm.ent.gz | 164.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ukm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ukm_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 3ukm_full_validation.pdf.gz | 517.8 KB | Display | |
Data in XML | 3ukm_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 3ukm_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/3ukm ftp://data.pdbj.org/pub/pdb/validation_reports/uk/3ukm | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 31910.986 Da / Num. of mol.: 4 / Fragment: UNP residues 19-288 / Mutation: W21T, C22M, N95Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HOHO1, K2P1 (TWIK-1), KCNK1, KCNO1, TWIK1 / Production host: Komagataella pastoris (fungus) / References: UniProt: O00180 #2: Chemical | ChemComp-UND / #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% Peg 400, 150 mM KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2011 |
Radiation | Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 32855 / Num. obs: 32855 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Rsym value: 0.057 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1628 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 3.4→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 153625.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 131.864 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 185.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.4→19.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.52 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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