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Yorodumi- PDB-2mri: Solution structure of a proteasome related subunit C terminal domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mri | ||||||
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Title | Solution structure of a proteasome related subunit C terminal domain | ||||||
Components | 26S proteasome regulatory subunit RPN9 | ||||||
Keywords | PROTEIN BINDING / hydrolase | ||||||
Function / homology | Function and homology information proteasome regulatory particle, lid subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome storage granule / proteasome assembly / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...proteasome regulatory particle, lid subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome storage granule / proteasome assembly / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / structural molecule activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Wu, Y. / Hu, Y. / Jin, C. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2015 Title: Solution structure of yeast Rpn9: insights into proteasome lid assembly. Authors: Hu, Y. / Wu, Y. / Li, Q. / Zhang, W. / Jin, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mri.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mri.ent.gz | 967.5 KB | Display | PDB format |
PDBx/mmJSON format | 2mri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/2mri ftp://data.pdbj.org/pub/pdb/validation_reports/mr/2mri | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20247.357 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 181-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: RPN9, NAS7, YDR427W, D9461.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04062 |
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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: 0.5mM [U-100% 13C, U-100% 15N] Protein-1, 20mM TRIS-2, 50mM sodium chloride-3, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.07 / pH: 7.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: AMBER Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |