+Open data
-Basic information
Entry | Database: PDB / ID: 6iim | ||||||
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Title | USP14 catalytic domain with IU1-206 | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 14 | ||||||
Keywords | HYDROLASE / USP14 inhibitor complex / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex ...negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex / Regulation of NF-kappa B signaling / cytoplasmic vesicle / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / innate immune response / synapse / cell surface / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Mei, Z.Q. / Wang, J.W. / Wang, F. / Wang, Y.W. | ||||||
Citation | Journal: Cell Res. / Year: 2018 Title: Small molecule inhibitors reveal allosteric regulation of USP14 via steric blockade. Authors: Wang, Y. / Jiang, Y. / Ding, S. / Li, J. / Song, N. / Ren, Y. / Hong, D. / Wu, C. / Li, B. / Wang, F. / He, W. / Wang, J. / Mei, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iim.cif.gz | 293.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iim.ent.gz | 238.2 KB | Display | PDB format |
PDBx/mmJSON format | 6iim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iim_validation.pdf.gz | 870.5 KB | Display | wwPDB validaton report |
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Full document | 6iim_full_validation.pdf.gz | 882.5 KB | Display | |
Data in XML | 6iim_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 6iim_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/6iim ftp://data.pdbj.org/pub/pdb/validation_reports/ii/6iim | HTTPS FTP |
-Related structure data
Related structure data | 6iikC 6iilC 6iinC 2aynS 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: 45604.762 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP14, TGT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54578, ubiquitinyl hydrolase 1 #2: Chemical | #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: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NH4F, Cscl, glycine |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.984 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Nov 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→30 Å / Num. obs: 48730 / % possible obs: 95.89 % / Redundancy: 3.1 % / Net I/σ(I): 19.46 |
Reflection shell | Resolution: 2.21→2.29 Å / Num. unique obs: 4594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AYN Resolution: 2.21→30 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→30 Å
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Refine LS restraints |
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LS refinement shell |
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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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