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Yorodumi- PDB-6f98: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f98 | ||||||
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Title | Solution structure of the RING domain of the E3 ubiquitin ligase HRD1 | ||||||
Components | E3 ubiquitin-protein ligase | ||||||
Keywords | LIGASE / RING domain / ubiquitin | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kniss, A. / Kazemi, S. / Lohr, F. / Guntert, P. / Dotsch, V. | ||||||
Citation | Journal: To Be Published Title: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1 Authors: Kniss, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f98.cif.gz | 481.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f98.ent.gz | 405 KB | Display | PDB format |
PDBx/mmJSON format | 6f98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f98 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f98 | HTTPS FTP |
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-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 | Mass: 8985.388 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HRD1, SCKG_1066 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A250WAY8 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.8 mM [U-98% 13C; U-98% 15N] E3 ubiquitin ligase Hrd1, 95% H2O/5% D2O Details: 25 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM TCEP, protease inhibitor cocktail, NaN3, DSS, 5% D2O Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.8 mM / Component: E3 ubiquitin ligase Hrd1 / Isotopic labeling: [U-98% 13C; U-98% 15N] |
Sample conditions | Ionic strength: 150 mM / Label: condition_1 / pH: 7.0 / Pressure: AMBIENT bar / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: Zinc included | ||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |