+Open data
-Basic information
Entry | Database: PDB / ID: 2qiy | ||||||
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Title | yeast Deubiquitinase Ubp3 and Bre5 cofactor complex | ||||||
Components |
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Keywords | Signaling protein/hydrolase / deubiquitylation / ubiquitin-specific processing proteases(UBPs) / NTF2 / protein-protein recognition / Hydrolase / Thiol protease / Ubl conjugation pathway / Phosphorylation / RNA-binding / Signaling protein-hydrolase COMPLEX | ||||||
Function / homology | Function and homology information Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / regulation of ER to Golgi vesicle-mediated transport / protein retention in Golgi apparatus / regulation of response to osmotic stress / Termination of translesion DNA synthesis / negative regulation of mitophagy / protein deubiquitination / stress granule assembly ...Ubp3-Bre5 deubiquitination complex / regulation of retrograde vesicle-mediated transport, Golgi to ER / ribophagy / regulation of ER to Golgi vesicle-mediated transport / protein retention in Golgi apparatus / regulation of response to osmotic stress / Termination of translesion DNA synthesis / negative regulation of mitophagy / protein deubiquitination / stress granule assembly / P-body / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / ribonucleoprotein complex / cysteine-type endopeptidase activity / mRNA binding / mitochondrion / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Li, K. / Liu, X. / Marmorstein, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating enzyme. Authors: Li, K. / Ossareh-Nazari, B. / Liu, X. / Dargemont, C. / Marmorstein, R. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Structural basis for interaction between the Ubp3 deubiqutinating enzyme and its Bre5 cofactor Authors: Li, K. / Zhao, K. / Ossareh-Nazari, B. / Da, G. / Dargemont, C. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qiy.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qiy.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qiy_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 2qiy_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 2qiy_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2qiy_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/2qiy ftp://data.pdbj.org/pub/pdb/validation_reports/qi/2qiy | HTTPS FTP |
-Related structure data
Related structure data | 1zx2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17675.080 Da / Num. of mol.: 2 / Fragment: residues 1-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: BRE5 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53741 #2: Protein/peptide | Mass: 5273.989 Da / Num. of mol.: 2 / Fragment: residues 190-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBP3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01477, EC: 3.1.2.15 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.27 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 9 Details: 10%(w/v) PEG 20000, 100mM Bicine, 2% Dioxan, pH 9.0, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9176 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→49.45 Å / Num. all: 59376 / Num. obs: 50599 / Redundancy: 3.9 % |
Reflection shell | Resolution: 1.69→1.75 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1ZX2 Resolution: 1.69→49.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.354 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→49.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.735 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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