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- PDB-7wf4: Composite map of human Kv1.3 channel in dalazatide-bound state wi... -
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Basic information
Entry | Database: PDB / ID: 7wf4 | |||||||||
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Title | Composite map of human Kv1.3 channel in dalazatide-bound state with beta subunits | |||||||||
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![]() | MEMBRANE PROTEIN / Ion channel / Kv channel / Potassium channel / Peptide toxin / ShK / Dalazatide / Selectivity filter / Molecular dynamics simulation | |||||||||
Function / homology | ![]() pinceau fiber / regulation of action potential / NADPH oxidation / regulation of protein localization to cell surface / corpus callosum development / voltage-gated monoatomic ion channel activity / aldo-keto reductase (NADPH) activity / Voltage gated Potassium channels / juxtaparanode region of axon / regulation of potassium ion transmembrane transport ...pinceau fiber / regulation of action potential / NADPH oxidation / regulation of protein localization to cell surface / corpus callosum development / voltage-gated monoatomic ion channel activity / aldo-keto reductase (NADPH) activity / Voltage gated Potassium channels / juxtaparanode region of axon / regulation of potassium ion transmembrane transport / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / optic nerve development / voltage-gated potassium channel activity / calyx of Held / tertiary granule membrane / potassium channel regulator activity / specific granule membrane / potassium ion transmembrane transport / voltage-gated potassium channel complex / extrinsic component of cytoplasmic side of plasma membrane / potassium ion transport / protein homooligomerization / cytoplasmic side of plasma membrane / presynaptic membrane / postsynaptic membrane / transmembrane transporter binding / cytoskeleton / membrane raft / axon / glutamatergic synapse / synapse / Neutrophil degranulation / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Tyagi, A. / Ahmed, T. / Jian, S. / Bajaj, S. / Ong, S.T. / Goay, S.S.M. / Zhao, Y. / Vorobyov, I. / Tian, C. / Chandy, K.G. / Bhushan, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rearrangement of a unique Kv1.3 selectivity filter conformation upon binding of a drug. Authors: Anu Tyagi / Tofayel Ahmed / Shi Jian / Saumya Bajaj / Seow Theng Ong / Stephanie Shee Min Goay / Yue Zhao / Igor Vorobyov / Changlin Tian / K George Chandy / Shashi Bhushan / ![]() ![]() ![]() ![]() Abstract: We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the ...We report two structures of the human voltage-gated potassium channel (Kv) Kv1.3 in immune cells alone (apo-Kv1.3) and bound to an immunomodulatory drug called dalazatide (dalazatide-Kv1.3). Both the apo-Kv1.3 and dalazatide-Kv1.3 structures are in an activated state based on their depolarized voltage sensor and open inner gate. In apo-Kv1.3, the aromatic residue in the signature sequence (Y447) adopts a position that diverges 11 Å from other K channels. The outer pore is significantly rearranged, causing widening of the selectivity filter and perturbation of ion binding within the filter. This conformation is stabilized by a network of intrasubunit hydrogen bonds. In dalazatide-Kv1.3, binding of dalazatide to the channel's outer vestibule narrows the selectivity filter, Y447 occupies a position seen in other K channels, and this conformation is stabilized by a network of intersubunit hydrogen bonds. These remarkable rearrangements in the selectivity filter underlie Kv1.3's transition into the drug-blocked state. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 481.5 KB | Display | ![]() |
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PDB format | ![]() | 406.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 74.1 KB | Display | |
Data in CIF | ![]() | 109.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32460MC ![]() 7wf3C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Potassium voltage-gated channel subfamily A member ... , 2 types, 8 molecules DBFHJNOP
#1: Protein | Mass: 31460.467 Da / Num. of mol.: 4 / Fragment: TM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 12777.475 Da / Num. of mol.: 4 / Fragment: T1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 4 molecules GIMo
#2: Protein | Mass: 36704.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13303, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 3 types, 107 molecules ![](data/chem/img/NAP.gif)
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#4: Chemical | ChemComp-NAP / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153218 / Symmetry type: POINT |