+Open data
-Basic information
Entry | Database: PDB / ID: 5lru | |||||||||
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Title | Structure of Cezanne/OTUD7B OTU domain | |||||||||
Components | OTU domain-containing protein 7B | |||||||||
Keywords | HYDROLASE / protease / deubiquitinase / OTU domain | |||||||||
Function / homology | Function and homology information mucosal immune response / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of canonical NF-kappaB signal transduction ...mucosal immune response / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Ovarian tumor domain proteases / in utero embryonic development / adaptive immune response / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / negative regulation of transcription by RNA polymerase II / proteolysis / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Mevissen, T.E.T. / Kulathu, Y. / Mulder, M.P.C. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D.M. / Akutsu, M. ...Mevissen, T.E.T. / Kulathu, Y. / Mulder, M.P.C. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D.M. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S.M.V. / Ovaa, H. / Komander, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2016 Title: Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Authors: Mevissen, T.E. / Kulathu, Y. / Mulder, M.P. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S. ...Authors: Mevissen, T.E. / Kulathu, Y. / Mulder, M.P. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S.M. / Ovaa, H. / Komander, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lru.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lru.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lru ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lru | HTTPS FTP |
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-Related 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: 36360.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OTUD7B, ZA20D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GQQ9, ubiquitinyl hydrolase 1 |
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#2: 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: 3.31 Å3/Da / Density % sol: 62.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 6.1), 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→90.2 Å / Num. obs: 25409 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→73.079 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→73.079 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.589 Å / Origin y: 9.7271 Å / Origin z: -12.7548 Å
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Refinement TLS group | Selection details: chain 'A' |