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Yorodumi- PDB-1vcs: Solution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vcs | ||||||
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Title | Solution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a [Mus musculus] | ||||||
Components | Vesicle transport through interaction with t-SNAREs homolog 1A | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SNARE / Habc domain / Vti1 / up and down three helix bundle / left-handed twist / vesicle transport / membrane fusion / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Golgi ribbon formation / Golgi to vacuole transport / voluntary musculoskeletal movement / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport ...synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Golgi ribbon formation / Golgi to vacuole transport / voluntary musculoskeletal movement / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / protein targeting to vacuole / neuron projection terminus / retrograde transport, endosome to Golgi / clathrin-coated vesicle / autophagosome / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / ER to Golgi transport vesicle membrane / autophagy / synaptic vesicle / late endosome membrane / membrane => GO:0016020 / endosome / Golgi membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dyanamics | ||||||
Authors | Abe, T. / Hirota, H. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a [Mus musculus] Authors: Abe, T. / Hirota, H. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vcs.cif.gz | 620.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vcs.ent.gz | 519.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/1vcs ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vcs | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11466.877 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 6-94) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system Gene: Mus musculus adult male lung cDNA, RIKEN full-length enriched library, clone:1200014A22 product: Vti1a (amino acid 6-94) Plasmid: P030825-55 / References: UniProt: O89116 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.0mM RSGI RUH-009 U-15N, 13C; 20mM d-Tris-HCl buffer; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dyanamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy and target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |