+Open data
-Basic information
Entry | Database: PDB / ID: 6wlv | ||||||
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Title | TASK2 in MSP1D1 lipid nanodisc at pH 6.5 | ||||||
Components | Potassium channel TASK2 | ||||||
Keywords | TRANSPORT PROTEIN / Potassium ion channel / K2P channel | ||||||
Function / homology | Function and homology information Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion export across plasma membrane / regulation of resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / potassium channel activity / potassium ion transmembrane transport ...Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion export across plasma membrane / regulation of resting membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / voltage-gated potassium channel activity / potassium ion import across plasma membrane / potassium channel activity / potassium ion transmembrane transport / potassium ion transport / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
Authors | Li, B. / Brohawn, S.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2020 Title: Structural basis for pH gating of the two-pore domain K channel TASK2. Authors: Baobin Li / Robert A Rietmeijer / Stephen G Brohawn / Abstract: TASK2 (also known as KCNK5) channels generate pH-gated leak-type K currents to control cellular electrical excitability. TASK2 is involved in the regulation of breathing by chemosensory neurons of ...TASK2 (also known as KCNK5) channels generate pH-gated leak-type K currents to control cellular electrical excitability. TASK2 is involved in the regulation of breathing by chemosensory neurons of the retrotrapezoid nucleus in the brainstem and pH homeostasis by kidney proximal tubule cells. These roles depend on channel activation by intracellular and extracellular alkalization, but the mechanistic basis for TASK2 gating by pH is unknown. Here we present cryo-electron microscopy structures of Mus musculus TASK2 in lipid nanodiscs in open and closed conformations. We identify two gates, distinct from previously observed K channel gates, controlled by stimuli on either side of the membrane. Intracellular gating involves lysine protonation on inner helices and the formation of a protein seal between the cytoplasm and the channel. Extracellular gating involves arginine protonation on the channel surface and correlated conformational changes that displace the K-selectivity filter to render it nonconductive. These results explain how internal and external protons control intracellular and selectivity filter gates to modulate TASK2 activity. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wlv.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wlv.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 6wlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wlv_validation.pdf.gz | 751.9 KB | Display | wwPDB validaton report |
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Full document | 6wlv_full_validation.pdf.gz | 758 KB | Display | |
Data in XML | 6wlv_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6wlv_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/6wlv ftp://data.pdbj.org/pub/pdb/validation_reports/wl/6wlv | HTTPS FTP |
-Related structure data
Related structure data | 21843MC 6wm0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10423 (Title: TASK2 in MSP1D1 lipid nanodisc at pH6.5 / Data size: 2.0 TB Data #1: multi-frame micrographs for ion channel TASK2 in closed state [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 38533.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk5 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9JK62 #2: Chemical | 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 |
-Sample preparation
Component | Name: TASK2 in MSP1D1 lipid nanodisc at pH 6.5 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.077 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | ||||||||||||||||||||
Source (recombinant) | Organism: Komagataella pastoris (fungus) | ||||||||||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Incubate 5 seconds, blot 3s seconds, blot force 1 |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.11 sec. / Electron dose: 0.98714 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2683 |
Image scans | Width: 11520 / Height: 8184 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3563337 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255808 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 151.61 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.88 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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