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Yorodumi- PDB-1pgy: Solution structure of the UBA domain in Saccharomyces cerevisiae ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pgy | ||||||
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Title | Solution structure of the UBA domain in Saccharomyces cerevisiae protein, Swa2p | ||||||
Components | Swa2p | ||||||
Keywords | PROTEIN BINDING / UBA / ubiquitin / Swa2 / auxilin / ubiquitin-associated domain | ||||||
Function / homology | Function and homology information Clathrin-mediated endocytosis / endoplasmic reticulum inheritance / clathrin coat disassembly / clathrin-dependent endocytosis / positive regulation of ATP-dependent activity / clathrin binding / receptor-mediated endocytosis / ubiquitin binding / vesicle / intracellular membrane-bounded organelle ...Clathrin-mediated endocytosis / endoplasmic reticulum inheritance / clathrin coat disassembly / clathrin-dependent endocytosis / positive regulation of ATP-dependent activity / clathrin binding / receptor-mediated endocytosis / ubiquitin binding / vesicle / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Chim, N. / Gall, W.E. / Xiao, J. / Harris, M.P. / Graham, T.R. / Krezel, A.M. | ||||||
Citation | Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004 Title: Solution structure of the ubiquitin-binding domain in Swa2p from Saccharomyces cerevisiae. Authors: Chim, N. / Gall, W.E. / Xiao, J. / Harris, M.P. / Graham, T.R. / Krezel, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pgy.cif.gz | 300.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pgy.ent.gz | 260.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pgy ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pgy | HTTPS FTP |
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-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/peptide | Mass: 5547.265 Da / Num. of mol.: 1 / Fragment: Ubiquitin-associated (UBA) domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SWA2 / Plasmid: pET32-EkLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06677 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM phosphate buffer / pH: 6.0 / Pressure: ambient / Temperature: 303 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: 373 NOE-derived distance constraints, 34 residual dipolar couplings | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 |