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Yorodumi- PDB-5oe7: Structure of OTULIN bound to the Met1-linked diubiquitin activity... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oe7 | ||||||
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Title | Structure of OTULIN bound to the Met1-linked diubiquitin activity probe | ||||||
Components |
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Keywords | HYDROLASE / deubiquitinase complex OTU | ||||||
Function / homology | Function and homology information protein linear deubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E ...protein linear deubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Termination of translesion DNA synthesis / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Stabilization of p53 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Authors | Elliott, P.R. / Komander, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell Chem Biol / Year: 2017 Title: A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN. Authors: Weber, A. / Elliott, P.R. / Pinto-Fernandez, A. / Bonham, S. / Kessler, B.M. / Komander, D. / El Oualid, F. / Krappmann, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oe7.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oe7.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 5oe7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/5oe7 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oe7 | HTTPS FTP |
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-Related structure data
Related structure data | 3znzS 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: 31726.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OTULIN, FAM105B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96BN8, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 16492.857 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Contains an N-terminal biotin-Ahx group. DRB is derived from the non-natural amino acid dihyrdoalanine, incorporated via chemical synthesis. Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG48 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 1.9-2.1 M Ammonium sulphate, 100 mM bis-tris / PH range: 6.3-6.6 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→54.43 Å / Num. obs: 11908 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.769 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZNZ Resolution: 2.95→54.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.888 / SU B: 63.789 / SU ML: 0.481 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.823 / ESU R Free: 0.485 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→54.43 Å
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