+Open data
-Basic information
Entry | Database: PDB / ID: 4i6l | ||||||
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Title | Crystal structure of OTUB1 in complex with ubiquitin variant | ||||||
Components |
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Keywords | HYDROLASE / deubiquitinase | ||||||
Function / homology | Function and homology information ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / protein K48-linked deubiquitination / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants ...ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / protein K48-linked deubiquitination / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / 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 / positive regulation of TORC1 signaling / 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 / 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) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / 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 / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Defective CFTR causes cystic fibrosis / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / Negative regulation of FGFR4 signaling / Stabilization of p53 / EGFR downregulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å | ||||||
Authors | Juang, Y.C. / Sicheri, F. | ||||||
Citation | Journal: Science / Year: 2013 Title: A strategy for modulation of enzymes in the ubiquitin system. Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / ...Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / Juang, Y.C. / Landry, M.C. / Yeh, C. / Zeqiraj, E. / Karamboulas, K. / Allali-Hassani, A. / Vedadi, M. / Tyers, M. / Moffat, J. / Sicheri, F. / Pelletier, L. / Durocher, D. / Raught, B. / Rotin, D. / Yang, J. / Moran, M.F. / Dhe-Paganon, S. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6l.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6l.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 4i6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6l ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6l | HTTPS FTP |
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-Related structure data
Related structure data | 3i3tC 3mtnC 3n3kC 3v6eC 1ubqS 2zfyS 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: 26572.781 Da / Num. of mol.: 1 / Fragment: UNP residues 45-271 / Mutation: C91S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB1, OTB1, OTU1, HSPC263 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FW1, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 8760.101 Da / Num. of mol.: 1 / Fragment: UNP residues 77-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48 |
#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: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, and 20% (w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 13269 / Num. obs: 12681 / Observed criterion σ(I): 2.4 |
Reflection shell | Resolution: 2.59→2.69 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zfy, 1ubq Resolution: 2.488→46.222 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 25.12 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.123 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.488→46.222 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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