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Yorodumi- PDB-6swr: Crystal structure of the lysosomal potassium channel MtTMEM175 T3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6swr | |||||||||
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Title | Crystal structure of the lysosomal potassium channel MtTMEM175 T38A mutant soaked with zinc | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / lysosome / TMEM175 / potassium channel / Parkinson disease | |||||||||
Function / homology | Function and homology information potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...potassium ion leak channel activity / proton channel activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / protein homotetramerization / periplasmic space / DNA damage response / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Lama glama (llama) Escherichia coli (E. coli) Marivirga tractuosa | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Brunner, J.D. / Jakob, R.P. / Schulze, T. / Neldner, Y. / Moroni, A. / Thiel, G. / Maier, T. / Schenck, S. | |||||||||
Citation | Journal: Elife / Year: 2020 Title: Structural basis for ion selectivity in TMEM175 K + channels. Authors: Brunner, J.D. / Jakob, R.P. / Schulze, T. / Neldner, Y. / Moroni, A. / Thiel, G. / Maier, T. / Schenck, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6swr.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6swr.ent.gz | 919.1 KB | Display | PDB format |
PDBx/mmJSON format | 6swr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6swr ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6swr | HTTPS FTP |
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-Related structure data
Related structure data | 6hd8C 6hd9C 6hdaC 6hdbC 6hdcC 1anfS 5jqhS 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
-Antibody / Protein , 2 types, 4 molecules ADBE
#1: Antibody | Mass: 53267.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama), (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: malE, b4034, JW3994 / Plasmid: pBXNPHM3 / Strain: K12 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AEX9 #2: Protein | Mass: 29450.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marivirga tractuosa (strain ATCC 23168 / DSM 4126 / NBRC 15989 / NCIMB 1408 / VKM B-1430 / H-43) (bacteria) Strain: ATCC 23168 / DSM 4126 / NBRC 15989 / NCIMB 1408 / VKM B-1430 / H-43 Gene: Ftrac_2467 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: E4TN31 |
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-Sugars , 2 types, 4 molecules
#3: Polysaccharide | #4: Sugar | |
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-Non-polymers , 2 types, 32 molecules
#5: Chemical | ChemComp-K / |
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#6: Water | ChemComp-HOH / |
-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: 4.24 Å3/Da / Density % sol: 70.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-HCl pH 8.5, 150 mM NaCl, 150 mM MgCl2 and 28-30 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.280961 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.280961 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.72 Å / Num. obs: 43526 / % possible obs: 99.8 % / Redundancy: 51.8 % / Biso Wilson estimate: 76.29 Å2 / CC1/2: 0.993 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.2→3.32 Å / Num. unique obs: 4510 / CC1/2: 0.663 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF, 5JQH Resolution: 3.2→49.72 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.2→49.72 Å
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