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Yorodumi- PDB-5wie: Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wie | |||||||||
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Title | Crystal structure of a Kv1.2-2.1 chimera K+ channel V406W mutant in an inactivated state | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / METAL TRANSPORT / Ion Channel / Inactivation / Voltage-gated | |||||||||
Function / homology | Function and homology information Voltage gated Potassium channels / 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 ...Voltage gated Potassium channels / 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 / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / aldo-keto reductase (NADPH) activity / 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 / regulation of monoatomic ion transmembrane transport / myoblast differentiation / neuromuscular process / Neutrophil degranulation / optic nerve development / regulation of dopamine secretion / neuronal cell body membrane / plasma membrane => GO:0005886 / 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 / membrane => GO:0016020 / 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) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Pau, V. / Zhou, Y. / Ramu, Y. / Xu, Y. / Lu, Z. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Crystal structure of an inactivated mutant mammalian voltage-gated K(+) channel. Authors: Pau, V. / Zhou, Y. / Ramu, Y. / Xu, Y. / Lu, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wie.cif.gz | 296.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wie.ent.gz | 228.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wie ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wie | HTTPS FTP |
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-Related structure data
Related structure data | 2r9rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Plasmid: pPICZ-C / Production host: Pichia (fungus) References: UniProt: P62483, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Protein | Mass: 60455.312 Da / Num. of mol.: 2 / Mutation: V406W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse) Gene: Kcna2 / Plasmid: pPICZ-C / Production host: Pichia (fungus) / References: UniProt: P63142, UniProt: P63141 #3: Chemical | #4: Chemical | ChemComp-PGW / ( #5: Chemical | ChemComp-K / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 73.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 50 mM Tris-Cl pH 8.3, 29-31% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 45103 / % possible obs: 99.5 % / Redundancy: 11.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.11 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.604 / Rpim(I) all: 0.413 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R9R Resolution: 3.3→40 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
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