[English] 日本語
Yorodumi- PDB-7sit: Crystal structure of Voltage gated potassium ion channel, Kv 1.2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sit | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Voltage gated potassium ion channel, Kv 1.2 chimera-3m | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / OXIDOREDUCTASE / Ion channel / C-type inactivation / Voltage gated Potassium ion channel / Chimera | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å | ||||||
Authors | Reddi, R. / Matulef, K. / Riederer, E.A. / Whorton, M.R. / Valiyaveetil, F.I. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Sci Adv / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7sit.cif.gz | 280.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7sit.ent.gz | 217.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sit_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7sit_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7sit_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 7sit_validation.cif.gz | 62.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/7sit ftp://data.pdbj.org/pub/pdb/validation_reports/si/7sit | HTTPS FTP |
-Related structure data
Related structure data | 7sizC 2r9rS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37353.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Komagataella pastoris (fungus) 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.) Rattus norvegicus (Norway rat) / Production host: Komagataella pastoris (fungus) #3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-O / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.53 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
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: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|