+Open data
-Basic information
Entry | Database: PDB / ID: 6w8a | ||||||
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Title | K2P2.1 (TREK-1):ML335 complex, 10 mM K+ | ||||||
Components | Potassium channel subfamily K member 2 | ||||||
Keywords | METAL TRANSPORT / ion channel / K2P / TREK1 / TREK-1 | ||||||
Function / homology | Function and homology information TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity ...TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / positive regulation of cellular response to hypoxia / cardiac ventricle development / stabilization of membrane potential / potassium ion leak channel activity / negative regulation of cardiac muscle cell proliferation / astrocyte projection / potassium channel inhibitor activity / outward rectifier potassium channel activity / negative regulation of DNA biosynthetic process / cochlea development / voltage-gated potassium channel activity / calyx of Held / response to axon injury / voltage-gated potassium channel complex / axon terminus / response to mechanical stimulus / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / memory / cellular response to hypoxia / apical plasma membrane / G protein-coupled receptor signaling pathway / axon / neuronal cell body / cell surface / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å | ||||||
Authors | Lolicato, M. / Minor, D.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. Authors: Lolicato, M. / Natale, A.M. / Abderemane-Ali, F. / Crottes, D. / Capponi, S. / Duman, R. / Wagner, A. / Rosenberg, J.M. / Grabe, M. / Minor Jr., D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w8a.cif.gz | 249.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w8a.ent.gz | 200.9 KB | Display | PDB format |
PDBx/mmJSON format | 6w8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/6w8a ftp://data.pdbj.org/pub/pdb/validation_reports/w8/6w8a | HTTPS FTP |
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-Related structure data
Related structure data | 6w7bC 6w7cC 6w7dC 6w7eC 6w82C 6w83C 6w84C 6w85C 6w86C 6w87C 6w88C 6w8cC 6w8fC 6cq6S C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34303.938 Da / Num. of mol.: 2 Mutation: K84R, Q85E, T86K, I88L, A89R, Q90A, A92P, N95S, S96D, T97Q, N119A, S300A, E306A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnk2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P97438 |
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-Non-polymers , 7 types, 23 molecules
#2: Chemical | ChemComp-K / #3: Chemical | #4: Chemical | ChemComp-16C / | #5: Chemical | ChemComp-R16 / #6: Chemical | ChemComp-CD / #7: Chemical | ChemComp-LNK / | #8: Chemical | ChemComp-D12 / | |
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-Details
Has ligand of interest | Y |
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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: 3.78 Å3/Da / Density % sol: 67.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22-25% PEG400, 100mM HEPES pH=8.0, 1mM CdCl2, 200mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3→46.47 Å / Num. obs: 21415 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3→3.18 Å / Num. unique obs: 3357 / CC1/2: 0.108 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6cq6 Resolution: 3.002→15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.939 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.838 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.367
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Displacement parameters | Biso mean: 150.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.002→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.002→3.02 Å
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Refinement TLS params. | Origin x: 2.5515 Å / Origin y: -23.4454 Å / Origin z: -27.2576 Å
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Refinement TLS group | Selection details: { *|* } |