+Open data
-Basic information
Entry | Database: PDB / ID: 2a79 | ||||||
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Title | Mammalian Shaker Kv1.2 potassium channel- beta subunit complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / potassium channel / voltage sensor / voltage dependent / ion channel / Shaker / eukaryotic / Kv1.2 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Long, S.B. / Campbell, E.B. / MacKinnon, R. | ||||||
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. #1: Journal: Science / Year: 2005 Title: Voltage Sensor of Kv1.2: Structural Basis of Electromechanical Coupling Authors: Long, S.B. / Campbell, E.B. / MacKinnon, R. | ||||||
History |
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Remark 999 | SEQUENCE SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR DETAILS REGARDING POLY-UNKNOWN CHAINS C AND D ...SEQUENCE SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR DETAILS REGARDING POLY-UNKNOWN CHAINS C AND D AND THEIR RELATIONSHIP TO CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a79.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a79.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a79_validation.pdf.gz | 749 KB | Display | wwPDB validaton report |
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Full document | 2a79_full_validation.pdf.gz | 767.7 KB | Display | |
Data in XML | 2a79_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 2a79_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/2a79 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a79 | HTTPS FTP |
-Related structure data
Related structure data | 1exbS S: Starting model for refinement |
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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 on special symmetry positions |
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Details | The biological unit is a tetramer formed by applying the I4 crystallographic symmetry to the coordinates that are deposited. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37353.086 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 |
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#2: Protein | Mass: 56749.438 Da / Num. of mol.: 1 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 |
-Poly-unknown ... , 2 types, 2 molecules CD
#3: Protein | Mass: 4443.468 Da / Num. of mol.: 1 / Fragment: T1-S1 linker and S1 helix of the Kv1.2 channel Source method: isolated from a genetically manipulated source Details: Chain C consists of a polyglycine model for the T1-S1 linker and a polyalanine model for the S1 helix of Kv1.2. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus) |
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#4: Protein/peptide | Mass: 1805.216 Da / Num. of mol.: 1 / Fragment: S3 helix of the Kv1.2 channel Source method: isolated from a genetically manipulated source Details: Chain D consists of a polyalanine model for the S3 helix of Kv1.2. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus) |
-Non-polymers , 3 types, 90 molecules
#5: Chemical | ChemComp-NAP / | ||
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#6: Chemical | ChemComp-K / #7: 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: 4.47 Å3/Da / Density % sol: 68 % |
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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 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2005 / Details: NSLS X25 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 36056 / Num. obs: 36056 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.92 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3636 / Rsym value: 0.477 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EXB Resolution: 2.9→29.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4165737.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Some of the missing residues listed in remark 465 are actually the residues that comprise chains C and D. The authors state it is unclear how to align the residues of chains C and D to the ...Details: Some of the missing residues listed in remark 465 are actually the residues that comprise chains C and D. The authors state it is unclear how to align the residues of chains C and D to the sequence of chain B, so each stretch of density assigned chain IDs C and D is labelled as UNK for unknown residue and was modelled in refinement as alanine or glycine.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.2425 Å2 / ksol: 0.295433 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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