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Yorodumi- PDB-2r9r: Shaker family voltage dependent potassium channel (kv1.2-kv2.1 pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r9r | ||||||
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Title | Shaker family voltage dependent potassium channel (kv1.2-kv2.1 paddle chimera channel) in association with beta subunit | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / POTASSIUM CHANNEL / VOLTAGE SENSOR / VOLTAGE DEPENDENT / ION CHANNEL / SHAKER / EUKARYOTIC / KV1.2 / KV2.1 / PADDLE CHIMERA CHANNEL / Ion transport / Ionic channel / NADP / Phosphorylation / Potassium transport / Transport / Voltage-gated channel / PROTEIN TRANSPORT | ||||||
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 / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / extrinsic component of cytoplasmic side of plasma membrane / 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: 2.4 Å | ||||||
Authors | Long, S.B. / Tao, X. / Campbell, E.B. / Mackinnon, R. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Authors: Long, S.B. / Tao, X. / Campbell, E.B. / MacKinnon, R. #1: 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. | ||||||
History |
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Remark 999 | sequence sequence of chain B,H has not exact UNP database match. It is a chimeric protein of rat ...sequence sequence of chain B,H has not exact UNP database match. It is a chimeric protein of rat Kv1.2 and rat Kv2.1. Please refer to the primary citation for more details. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r9r.cif.gz | 313.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9r.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 2r9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9r ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9r | HTTPS FTP |
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-Related structure data
Related structure data | 2a79S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 AGBH
#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: Pichia pastoris (fungus) / References: UniProt: P62483 #2: Protein | Mass: 58821.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: kcna2 / Production host: Pichia pastoris (fungus) |
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-Non-polymers , 4 types, 346 molecules
#3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-PGW / ( #6: Water | ChemComp-HOH / | |
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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: 3.83 Å3/Da / Density % sol: 67.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: peg 400, potassium chloride, tris buffer, EDTA, DTT, TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2007 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 112726 / Num. obs: 112726 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 2.47 % / Biso Wilson estimate: 44.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 9974 / Rsym value: 0.436 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2A79 Resolution: 2.4→49.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5699592.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.3798 Å2 / ksol: 0.341816 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→49.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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