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Yorodumi- PDB-3eb4: Voltage-dependent K+ channel beta subunit (I211R) in complex with... -
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-Basic information
Entry | Database: PDB / ID: 3eb4 | ||||||
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Title | Voltage-dependent K+ channel beta subunit (I211R) in complex with cortisone | ||||||
Components | Voltage-gated potassium channel subunit beta-2 | ||||||
Keywords | TRANSPORT PROTEIN / oxidoreductase / kvbeta / cortisone / interface / Cytoplasm / Ion transport / Ionic channel / NADP / Phosphoprotein / Potassium / Potassium transport / Transport / Voltage-gated channel | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Pan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2008 Title: Cortisone dissociates the Shaker family K+ channels from their beta subunits. Authors: Pan, Y. / Weng, J. / Kabaleeswaran, V. / Li, H. / Cao, Y. / Bhosle, R.C. / Zhou, M. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Structure of a voltage-dependent K+ channel beta subunit. Authors: Gulbis, J.M. / Mann, S. / MacKinnon, R. #2: Journal: Science / Year: 2000 Title: Structure of the cytoplasmic beta subunit-T1 assembly of voltage-dependent K+ channels. Authors: Gulbis, J.M. / Zhou, M. / Mann, S. / MacKinnon, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eb4.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eb4.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 3eb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eb4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3eb4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3eb4_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3eb4_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3eb4 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3eb4 | HTTPS FTP |
-Related structure data
Related structure data | 3eauC 3eb3C 1exbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36616.227 Da / Num. of mol.: 1 / Fragment: cytoplasmic Kvbeta subunit / Mutation: I211R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / References: UniProt: P62483 |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-PDN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6-15% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 7.9 - 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 2007 |
Radiation | Monochromator: single Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 35198 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.045 / Net I/σ(I): 35.66 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.48 / Num. unique all: 3063 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1EXB, chain A, beta subunit Resolution: 2→40.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3391309.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.3035 Å2 / ksol: 0.35606 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→40.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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