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Yorodumi- PDB-5lrv: Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lrv | |||||||||
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Title | Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin | |||||||||
Components |
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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 / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination ...mucosal immune response / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / cysteine-type peptidase activity / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 5lrv.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lrv.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lrv ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lrv | 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
-Protein , 1 types, 1 molecules A
#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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-Polyubiquitin- ... , 2 types, 2 molecules BC
#2: Protein | Mass: 8547.770 Da / Num. of mol.: 1 / Mutation: K11X / Source method: obtained synthetically Details: Lys11 was replaced with a diaminobutyric acid (DAB) residue Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47 |
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#3: Protein | Mass: 8604.884 Da / Num. of mol.: 1 / Mutation: G76X / Source method: obtained synthetically Details: Gly76 was replaced with a ligation handle for diubiquitin probe generation Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47 |
-Non-polymers , 3 types, 8 molecules
#4: Chemical | ChemComp-PO4 / | ||
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#5: Chemical | ChemComp-GOL / #6: 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: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→56.52 Å / Num. obs: 11505 / % possible obs: 94.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.162 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.162 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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