+Open data
-Basic information
Entry | Database: PDB / ID: 4o8y | ||||||
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Title | Zinc-free Rpn11 in complex with Rpn8 | ||||||
Components |
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Keywords | HYDROLASE / MPN JAMM / deubiquitinase | ||||||
Function / homology | Function and homology information peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule ...peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule / proteasome assembly / Neutrophil degranulation / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrion / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Worden, E.J. / Padovani, C. / Martin, A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Authors: Worden, E.J. / Padovani, C. / Martin, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o8y.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o8y.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 4o8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/4o8y ftp://data.pdbj.org/pub/pdb/validation_reports/o8/4o8y | HTTPS FTP |
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-Related structure data
Related structure data | 4o8xC 2o95S 4f70S C: citing same article (ref.) 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: 21040.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RPN8, YOR261C, O5360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08723 | ||
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#2: Protein | Mass: 26893.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RPN11, MPR1, YFR004W / Production host: Escherichia coli (E. coli) / References: UniProt: P43588 | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% PEG8000, 30% ethylene glycol, and 100 mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 37562 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.986 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4F70, 2O95 Resolution: 1.95→40.615 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8841 / SU ML: 0.17 / σ(F): 0.1 / Phase error: 18.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.71 Å2 / Biso mean: 30.8519 Å2 / Biso min: 5.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40.615 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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