[English] 日本語
Yorodumi- PDB-3lut: A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lut | ||||||
---|---|---|---|---|---|---|---|
Title | A Structural Model for the Full-length Shaker Potassium Channel Kv1.2 | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / Voltage gating / potassium channel / Kv1.2 / gating charges / normal-mode analysis / Ion transport / Ionic channel / NADP / Phosphoprotein / Potassium / Potassium transport / Transport / Voltage-gated channel / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane | ||||||
Function / homology | Function and homology information optic nerve structural organization / pinceau fiber / regulation of action potential / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / NADPH oxidation / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep ...optic nerve structural organization / pinceau fiber / regulation of action potential / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / NADPH oxidation / paranodal junction / potassium ion export across plasma membrane / regulation of circadian sleep/wake cycle, non-REM sleep / axon initial segment / regulation of protein localization to cell surface / corpus callosum development / aldo-keto reductase (NADPH) activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / outward rectifier potassium channel 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 / delayed rectifier potassium channel activity / myoblast differentiation / neuromuscular process / Neutrophil degranulation / optic nerve development / regulation of dopamine secretion / neuronal cell body membrane / voltage-gated potassium channel activity / action potential / kinesin binding / lamellipodium membrane / calyx of Held / neuronal action potential / potassium channel regulator activity / hematopoietic progenitor cell differentiation / axon terminus / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / postsynaptic density membrane / protein homooligomerization / cytoplasmic side of plasma membrane / cerebral cortex development / lamellipodium / presynaptic membrane / postsynaptic membrane / perikaryon / transmembrane transporter binding / endosome / postsynaptic density / cytoskeleton / neuron projection / axon / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Chen, X. / Ni, F. / Wang, Q. / Ma, J. | ||||||
Citation | Journal: Science / Year: 2005 Title: Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel Authors: Long, S.B. / Campbell, E.B. / MacKinnon, R. #2: Journal: Nature / Year: 2007 Title: Atomic structure of a voltage-dependent K+ channel inalipidmembrane-like environment Authors: Long, S.B. / Tao, X. / Campbell, E.B. / Mackinnon, R. | ||||||
History |
| ||||||
Remark 0 | THIS ENTRY 3LUT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2A79SF) ... THIS ENTRY 3LUT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2A79SF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2A79: LONG,S.B., CAMPBELL,E.B., MACKINNON,R. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lut.cif.gz | 307.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lut.ent.gz | 251.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lut_validation.pdf.gz | 733.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3lut_full_validation.pdf.gz | 766.5 KB | Display | |
Data in XML | 3lut_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 3lut_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/3lut ftp://data.pdbj.org/pub/pdb/validation_reports/lu/3lut | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 41071.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Pichia pastoris (fungus) / References: UniProt: P62483 | ||
---|---|---|---|
#2: Protein | Mass: 56763.461 Da / Num. of mol.: 1 / Mutation: N207Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus) / References: UniProt: P63142 | ||
#3: Chemical | ChemComp-NAP / | ||
#4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.36 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2A79. |
---|
-Data collection
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.9→29.48 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.92 / SU B: 26.941 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 123.357 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
|