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Yorodumi- PDB-6hdc: Crystal structure of the potassium channel MtTMEM175 T38A variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hdc | |||||||||
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Title | Crystal structure of the potassium channel MtTMEM175 T38A variant in complex with a Nanobody-MBP fusion protein | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / lysosome / TMEM175 / potassium channel | |||||||||
Function / homology | Function and homology information proton channel activity / potassium ion leak channel activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...proton channel activity / potassium ion leak channel activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / 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 DSM 4126 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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. #1: Journal: Biorxiv / Year: 2019 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 | 6hdc.cif.gz | 562.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hdc.ent.gz | 472.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/6hdc ftp://data.pdbj.org/pub/pdb/validation_reports/hd/6hdc | HTTPS FTP |
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-Related structure data
Related structure data | 6hd8C 6hd9C 6hdaC 6hdbC 6swrC 1anfS 5jqhS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Antibody / Protein , 2 types, 2 molecules AB
#1: Antibody | Mass: 53267.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama), (gene. exp.) Escherichia coli (strain K12) (bacteria) Plasmid: pBXNPHM3 / Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AEX9 |
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#2: Protein | Mass: 29450.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marivirga tractuosa DSM 4126 (bacteria) Gene: Ftrac_2467 / Plasmid: pBXC3H / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: E4TN31 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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#4: Sugar | ChemComp-LMT / |
-Non-polymers , 2 types, 22 molecules
#5: Chemical | ChemComp-K / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.5 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 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: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→47.2 Å / Num. obs: 16953 / % possible obs: 99.9 % / Redundancy: 146 % / Biso Wilson estimate: 90.29 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.216 / Rrim(I) all: 0.255 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.4→3.67 Å / Redundancy: 144.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3435 / CC1/2: 0.797 / Rpim(I) all: 0.901 / Rrim(I) all: 1.0621 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF, 5JQH Resolution: 3.4→22.25 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.839 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.559
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Displacement parameters | Biso mean: 179.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→22.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.61 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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