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Yorodumi- PDB-8de8: Cryo-EM structure of the zebrafish two pore domain K+ channel TRE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8de8 | |||||||||
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Title | Cryo-EM structure of the zebrafish two pore domain K+ channel TREK1 (K2P2.1) in DDM/POPA mixed micelles | |||||||||
Components | Potassium channel, subfamily K, member 2a | |||||||||
Keywords | MEMBRANE PROTEIN / ion channel / K2P / K2P2.1 / TREK1 / TREK-1 / POPA | |||||||||
Function / homology | Chem-D21 / : / : Function and homology information | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
Authors | Schmidpeter, P.A.M. / Nimigean, C.M. / Riegelhaupt, P.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1. Authors: Philipp A M Schmidpeter / John T Petroff / Leila Khajoueinejad / Aboubacar Wague / Cheryl Frankfater / Wayland W L Cheng / Crina M Nimigean / Paul M Riegelhaupt / Abstract: Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within ...Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8de8.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8de8.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 8de8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8de8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8de8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8de8_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 8de8_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/8de8 ftp://data.pdbj.org/pub/pdb/validation_reports/de/8de8 | HTTPS FTP |
-Related structure data
Related structure data | 27387MC 8de7C 8de9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35559.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: kcnk2a / Production host: Komagataella pastoris (fungus) / References: UniProt: X1WC65 #2: Chemical | ChemComp-D21 / ( #3: Chemical | ChemComp-K / Has ligand of interest | Y | Has protein modification | 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: Potassium channel subfamily K member 2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Buffer solution | pH: 8 / Details: 150mM KCl, 20mM TRIS, 0.25mM DDM, 0.1mg/ml POPA |
Specimen | Conc.: 3 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: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 63.32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 492284 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303950 / Symmetry type: POINT |