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Yorodumi- PDB-6hh0: Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hh0 | ||||||
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Title | Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles | ||||||
Components | V-type proton ATPase subunit a, vacuolar isoform | ||||||
Keywords | MEMBRANE PROTEIN / ATPasse / transmembrane helix / DPC micelle / NMR spectroscopy | ||||||
Function / homology | Function and homology information protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response ...protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transport / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / ATPase binding / protein-containing complex assembly / membrane raft Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Zangger, K. / Hohlweg, W. / Wagner, G. | ||||||
Funding support | Austria, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A cation-pi interaction in a transmembrane helix of vacuolar ATPase retains the proton-transporting arginine in a hydrophobic environment. Authors: Hohlweg, W. / Wagner, G.E. / Hofbauer, H.F. / Sarkleti, F. / Setz, M. / Gubensak, N. / Lichtenegger, S. / Falsone, S.F. / Wolinski, H. / Kosol, S. / Oostenbrink, C. / Kohlwein, S.D. / Zangger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hh0.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hh0.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hh0_validation.pdf.gz | 494.2 KB | Display | wwPDB validaton report |
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Full document | 6hh0_full_validation.pdf.gz | 575.7 KB | Display | |
Data in XML | 6hh0_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6hh0_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hh0 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hh0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2832.328 Da / Num. of mol.: 1 / Fragment: transmembrane helix 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPH1, YOR270C / Production host: synthetic construct (others) / References: UniProt: P32563 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: micelle Contents: 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O Details: 100 mM deuterated DPC 50 mM KPi pH 5.0 / Label: partially 13C, 15N double labeled / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: condition / pH: 5.0 / Pressure: ambient atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 10 |