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Yorodumi- PDB-6gf1: The structure of the ubiquitin-like modifier FAT10 reveals a nove... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gf1 | ||||||
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Title | The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting mechanism for degradation by the 26S proteasome | ||||||
Components | Ubiquitin D | ||||||
Keywords | SIGNALING PROTEIN / Ubiquitin-like / degradation | ||||||
Function / homology | Function and homology information protein modification by small protein conjugation / myeloid dendritic cell differentiation / aggresome assembly / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to type II interferon / response to tumor necrosis factor / fibrillar center / Neddylation ...protein modification by small protein conjugation / myeloid dendritic cell differentiation / aggresome assembly / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to type II interferon / response to tumor necrosis factor / fibrillar center / Neddylation / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / positive regulation of apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.925 Å | ||||||
Authors | Aichem, A. / Anders, S. / Catone, N. / Roessler, P. / Stotz, S. / Berg, A. / Schwab, R. / Scheuermann, S. / Bialas, J. / Schmidtke, G. ...Aichem, A. / Anders, S. / Catone, N. / Roessler, P. / Stotz, S. / Berg, A. / Schwab, R. / Scheuermann, S. / Bialas, J. / Schmidtke, G. / Peter, C. / Groettrup, M. / Wiesner, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Authors: Aichem, A. / Anders, S. / Catone, N. / Stotz, S. / Berg, A. / Schwab, R. / Scheuermann, S. / Bialas, J. / Schutz-Stoffregen, M.C. / Schmidtke, G. / Peter, C. / Groettrup, M. / Wiesner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gf1.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gf1.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/6gf1 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gf1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9434.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: N Domain / Source: (gene. exp.) Homo sapiens (human) / Gene: UBD, FAT10 / Production host: Escherichia coli (E. coli) / References: UniProt: O15205 #2: Chemical | ChemComp-SO4 / #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: 3.89 Å3/Da / Density % sol: 68.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2 M Ammonium sulfate, 0.1 M Citric acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→43.254 Å / Num. obs: 64119 / % possible obs: 99.31 % / Redundancy: 10 % / Net I/σ(I): 21.38 |
Reflection shell | Resolution: 1.925→1.994 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.925→43.254 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.925→43.254 Å
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Refine LS restraints |
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LS refinement shell |
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