+Open data
-Basic information
Entry | Database: PDB / ID: 2n7e | ||||||
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Title | Solution structure of the UBL domain of yeast Ddi1 | ||||||
Components | DNA damage-inducible protein 1 | ||||||
Keywords | UNKNOWN FUNCTION / DDI1 | ||||||
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 / torsion angle dynamics, molecular dynamics | ||||||
Authors | Siva, M. / Grantz Saskova, K. / Veverka, V. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family. Authors: Trempe, J.F. / Saskova, K.G. / Siva, M. / Ratcliffe, C.D. / Veverka, V. / Hoegl, A. / Menade, M. / Feng, X. / Shenker, S. / Svoboda, M. / Kozisek, M. / Konvalinka, J. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n7e.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2n7e.ent.gz | 962.9 KB | Display | PDB format |
PDBx/mmJSON format | 2n7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/2n7e ftp://data.pdbj.org/pub/pdb/validation_reports/n7/2n7e | 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: 9691.938 Da / Num. of mol.: 1 / Fragment: UBL domain (UNP residues 1-80) 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) / 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 | Contents: 25 mM sodium phosphate, 100 mM sodium chloride, 0.4 mM [U-13C; U-15N] protein, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-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: torsion angle dynamics, molecular dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 43 |