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Yorodumi- PDB-4jta: Crystal structure of Kv1.2-2.1 paddle chimera channel in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jta | |||||||||
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Title | Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/toxin / potassium channel / pore blocking toxin / protein-protein complex / TRANSPORT PROTEIN-toxin complex | |||||||||
Function / homology | Function and homology information optic nerve structural organization / pinceau fiber / regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / positive regulation of norepinephrine secretion ...optic nerve structural organization / pinceau fiber / regulation of action potential / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / clustering of voltage-gated potassium channels / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / NADPH oxidation / paranodal junction / potassium ion export across plasma membrane / proximal dendrite / positive regulation of calcium ion-dependent exocytosis / regulation of circadian sleep/wake cycle, non-REM sleep / cholinergic synapse / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / delayed rectifier potassium channel activity / vesicle docking involved in exocytosis / glutamate receptor signaling pathway / myoblast differentiation / postsynaptic specialization membrane / neuromuscular process / Neutrophil degranulation / response to L-glutamate / optic nerve development / ion channel inhibitor activity / 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 / lateral plasma membrane / positive regulation of protein targeting to membrane / response to axon injury / potassium channel regulator activity / cellular response to nutrient levels / negative regulation of insulin secretion / defense response to fungus / hematopoietic progenitor cell differentiation / axon terminus / voltage-gated potassium channel complex / potassium ion transmembrane transport / sensory perception of pain / dendrite membrane / cellular response to calcium ion / potassium ion transport / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / postsynaptic density membrane / protein homooligomerization / cytoplasmic side of plasma membrane / sarcolemma / cerebral cortex development / glucose homeostasis / lamellipodium / presynaptic membrane / postsynaptic membrane / perikaryon / toxin activity / killing of cells of another organism / transmembrane transporter binding / endosome / postsynaptic density / cytoskeleton / defense response to bacterium / neuron projection / apical plasma membrane / protein heterodimerization activity / axon / neuronal cell body / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) Leiurus quinquestriatus hebraeus (scorpion) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | MacKinnon, R. / Banerjee, A. / Lee, A. / Campbell, E. | |||||||||
Citation | Journal: Elife / Year: 2013 Title: Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K(+) channel. Authors: Banerjee, A. / Lee, A. / Campbell, E. / Mackinnon, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jta.cif.gz | 319.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jta.ent.gz | 258.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jta_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4jta_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4jta_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 4jta_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/4jta ftp://data.pdbj.org/pub/pdb/validation_reports/jt/4jta | HTTPS FTP |
-Related structure data
-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 on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules APBQ
#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) / Genus: Rattus norvegicus / Species: 10116 / Strain: Ckbeta2, Kcnab2, Kcnb3 / Cell: Pichia pastoris / Cell line: 4922 / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Pichia pastoris (fungus) / References: UniProt: P62483 #2: Protein | Mass: 58821.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: This is a chimeric channel between Kv1.2 and Kv2.1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus norvegicus / Species: 10116 / Strain: Ckbeta2, Kcnab2, Kcnb3 / Cell: Pichia pastoris / Cell line: 4922 / Gene: Kcna2, Kcnb1 / Production host: Pichia pastoris (fungus) / References: UniProt: P63142, UniProt: P15387 |
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-Protein/peptide , 1 types, 1 molecules Y
#3: Protein/peptide | Mass: 4309.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leiurus quinquestriatus hebraeus (scorpion) Genus: Leiurus quinquestriatus hebraeus / Species: 6884 / Cell: Escherichia coli / Cell line: 562 / Production host: Escherichia coli (E. coli) / References: UniProt: P13487 |
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-Non-polymers , 4 types, 343 molecules
#4: Chemical | #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-PGW / ( #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ONE CHANNEL TETRAMER (GENERATED BY USING THE BIOMT TRANSFORMATIONS ON CHAINS P AND Q AS NOTED ABOVE) ...ONE CHANNEL TETRAMER (GENERATED BY USING THE BIOMT TRANSFORMA |
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Sequence details | PROTEIN IN CHAINS B,Q IS A CHIMERIC PROTEIN OF RAT KV1.2 AND RAT KV2.1. PLEASE REFER TO THE PRIMARY ...PROTEIN IN CHAINS B,Q IS A CHIMERIC PROTEIN OF RAT KV1.2 AND RAT KV2.1. PLEASE REFER TO THE PRIMARY CITATION FOR MORE DETAILS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 99907 / % possible obs: 96.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.075 / Χ2: 1.985 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 0.25 / σ(F): 0 Details: THERE IS A TOXIN MOLECULE BOUND TO THE CHANNEL TETRAMER GENERATED BY FOUR COPIES OF A TOGETHER WITH FOUR COPIES OF B. HOWEVER IT WAS NOT BUILT BECAUSE IT WAS NOT SUFFICIENTLY WELL ORDERED. ...Details: THERE IS A TOXIN MOLECULE BOUND TO THE CHANNEL TETRAMER GENERATED BY FOUR COPIES OF A TOGETHER WITH FOUR COPIES OF B. HOWEVER IT WAS NOT BUILT BECAUSE IT WAS NOT SUFFICIENTLY WELL ORDERED. RESIDUES 133-144 IN CHAIN B WAS BUILT AS A POLYGLYCINE CHAIN BECAUSE OF LACK OF ADEQUATE ELECTRON DENSITY FOR THE SIDE CHAINS.
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Solvent computation | Bsol: 72.2764 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 208.21 Å2 / Biso mean: 72.8609 Å2 / Biso min: 19.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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