+Open data
-Basic information
Entry | Database: PDB / ID: 6gha | ||||||
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Title | USP15 catalytic domain structure | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15 | ||||||
Keywords | HYDROLASE / protease / ubiquitin / ubiquitin specific protease | ||||||
Function / homology | Function and homology information regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination / transcription elongation-coupled chromatin remodeling / BMP signaling pathway / SMAD binding / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Ward, S.J. / Gratton, H.E. / Caulton, S.G. / Emsley, J. / Dreveny, I. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel. Authors: Ward, S.J. / Gratton, H.E. / Indrayudha, P. / Michavila, C. / Mukhopadhyay, R. / Maurer, S.K. / Caulton, S.G. / Emsley, J. / Dreveny, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gha.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gha.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 6gha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gha_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 6gha_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 6gha_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 6gha_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/6gha ftp://data.pdbj.org/pub/pdb/validation_reports/gh/6gha | HTTPS FTP |
-Related structure data
Related structure data | 6gh9C 2y6eS 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: 41747.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: USP15 catalytic core domain (D1D2) with the insert between the two sub-domains harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),USP15 ...Details: USP15 catalytic core domain (D1D2) with the insert between the two sub-domains harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),USP15 catalytic core domain (D1D2) with the insert between the two sub-domains harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),USP15 catalytic core domain (D1D2) with the insert between the two sub-domains harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO),USP15 catalytic core domain (D1D2) with the insert between the two sub-domains harbouring a predicted UBL domain replaced by a short linker (based on the USP8 structure PDB ID: 2GFO) Source: (gene. exp.) Homo sapiens (human) / Gene: USP15, KIAA0529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1 |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-Cl pH 8.5, 20% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.97→46.86 Å / Num. obs: 24858 / % possible obs: 97.3 % / Redundancy: 3 % / Biso Wilson estimate: 33.52 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.074 / Rrim(I) all: 0.134 / Net I/σ(I): 4.7 / Num. measured all: 73950 / Scaling rejects: 140 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y6E Resolution: 1.98→35.248 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.89 Å2 / Biso mean: 48.2582 Å2 / Biso min: 17.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→35.248 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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