+Open data
-Basic information
Entry | Database: PDB / ID: 6hel | |||||||||
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Title | Structure of human USP25 | |||||||||
Components | Ubiquitin carboxyl-terminal hydrolase 25 | |||||||||
Keywords | HYDROLASE / Ubiquitin / USP / Ubiquitin-specific protease / DUB / Deubiquitinase / protease / isopeptidase / USP25 | |||||||||
Function / homology | Function and homology information ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / regulation of protein stability / protein modification process / peptidase activity ...ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / regulation of protein stability / protein modification process / peptidase activity / ATPase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / ubiquitin protein ligase binding / endoplasmic reticulum / proteolysis / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.941 Å | |||||||||
Authors | Gersch, M. / Komander, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Mol.Cell / Year: 2019 Title: Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Authors: Gersch, M. / Wagstaff, J.L. / Toms, A.V. / Graves, B. / Freund, S.M.V. / Komander, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hel.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hel.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/6hel ftp://data.pdbj.org/pub/pdb/validation_reports/he/6hel | HTTPS FTP |
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-Related structure data
Related structure data | 6hehSC 6heiC 6hejC 6hekSC 6hemC S: Starting model for refinement C: citing same article (ref.) |
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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: 65082.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP25, USP21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLacI / References: UniProt: Q9UHP3, ubiquitinyl hydrolase 1 #2: 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: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12% (w/v) PEG 3350, 167 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→59.17 Å / Num. obs: 20988 / % possible obs: 93.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 103 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.94→3.39 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1050 / CC1/2: 0.501 / Rrim(I) all: 1.57 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HEH and 6HEK Resolution: 2.941→59.166 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.941→59.166 Å
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Refine LS restraints |
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LS refinement shell |
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