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Yorodumi- PDB-2k88: Association of subunit d (Vma6p) and E (Vma4p) with G (Vma10p) an... -
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-Basic information
Entry | Database: PDB / ID: 2k88 | ||||||
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Title | Association of subunit d (Vma6p) and E (Vma4p) with G (Vma10p) and the NMR solution structure of subunit G (G1-59) of the Saccharomyces cerevisiae V1VO ATPase | ||||||
Components | Vacuolar proton pump subunit G | ||||||
Keywords | HYDROLASE / G subunit / V1Vo ATPase / Vma10p / Hydrogen ion transport / Ion transport / Transport | ||||||
Function / homology | Function and homology information Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Golgi membrane / ATP hydrolysis activity Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Sankaranarayanan, N. / Gayen, S. / Thaker, Y. / Subramanian, V. / Manimekalai, M.S.S. / Gruber, G. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2009 Title: Assembly of subunit d (Vma6p) and G (Vma10p) and the NMR solution structure of subunit G (G(1-59)) of the Saccharomyces cerevisiae V(1)V(O) ATPase. Authors: Rishikesan, S. / Gayen, S. / Thaker, Y.R. / Vivekanandan, S. / Manimekalai, M.S. / Yau, Y.H. / Shochat, S.G. / Gruber, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k88.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k88.ent.gz | 167.6 KB | Display | PDB format |
PDBx/mmJSON format | 2k88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k88_validation.pdf.gz | 338.8 KB | Display | wwPDB validaton report |
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Full document | 2k88_full_validation.pdf.gz | 393 KB | Display | |
Data in XML | 2k88_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 2k88_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/2k88 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/2k88 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6969.021 Da / Num. of mol.: 1 / Fragment: G(1-59)subunit of V1Vo ATPase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VMA10, YHR039C-A, YHR039BC, YHR039C-B / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 References: UniProt: P48836, H+-transporting two-sector ATPase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 25 mM sodium phosphate, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 25 mM / Component: sodium phosphate |
Sample conditions | Ionic strength: 0 / pH: 6.8 / Pressure: AMBIENT / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 10 |