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- PDB-7sit: Crystal structure of Voltage gated potassium ion channel, Kv 1.2 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sit | ||||||
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Title | Crystal structure of Voltage gated potassium ion channel, Kv 1.2 chimera-3m | ||||||
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![]() | TRANSPORT PROTEIN / OXIDOREDUCTASE / Ion channel / C-type inactivation / Voltage gated Potassium ion channel / Chimera | ||||||
Function / homology | ![]() pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / regulation of action potential / Voltage gated Potassium channels / potassium channel complex / NADPH oxidation / axon initial segment / regulation of protein localization to cell surface / aldo-keto reductase (NADPH) activity / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / neuromuscular process / Neutrophil degranulation / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / axon terminus / voltage-gated potassium channel complex / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / protein-containing complex binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Reddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for C-type inactivation in a Shaker family voltage-gated K + channel. Authors: Reddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.1 KB | Display | ![]() |
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PDB format | ![]() | 217.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sizC ![]() 2r9rS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 37353.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Protein | Mass: 58823.617 Da / Num. of mol.: 2 Mutation: L15H, C31S, C32S, N207Q, W362F, S367T, V377T, C435S, C482S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-O / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris, pH 8.5, 28-32% PEG400, CHAPS / PH range: 8.3-8.8 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→49.16 Å / Num. obs: 35720 / % possible obs: 99.9 % / Redundancy: 14.9 % / CC1/2: 0.99 / CC star: 0.54 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.32→3.51 Å / Num. unique obs: 4588 / CC1/2: 0.54 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2R9R Resolution: 3.32→49.159 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 299.21 Å2 / Biso mean: 126.359 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.32→49.159 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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