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Yorodumi- PDB-2mr9: NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mr9 | ||||||
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Title | NMR structure of UBA domain of DNA-damage-inducible 1 protein (Ddi1) | ||||||
Components | DNA damage-inducible protein 1 | ||||||
Keywords | HYDROLASE / DNA-damage-inducible 1 protein / Ubiquitin associated domain / Ddi1 / UBA | ||||||
Function / homology | Function and homology information proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Zhang, D. / Fushman, D. | ||||||
Citation | Journal: Structure / Year: 2015 Title: DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin. Authors: Nowicka, U. / Zhang, D. / Walker, O. / Krutauz, D. / Castaneda, C.A. / Chaturvedi, A. / Chen, T.Y. / Reis, N. / Glickman, M.H. / Fushman, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mr9.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mr9.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 2mr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/2mr9 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/2mr9 | HTTPS FTP |
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-Related structure data
Related structure data | 2mroC 2mrpC 2mwsC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4745.367 Da / Num. of mol.: 1 / Fragment: Ubiquitin associated domain, UNP residues 389-428 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: DDI1, VSM1, YER143W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P40087 |
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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 |
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Sample conditions |
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-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: 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: 10 / Conformers submitted total number: 10 |