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Yorodumi- PDB-3znz: Crystal structure of OTULIN OTU domain (C129A) in complex with Me... -
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-Basic information
Entry | Database: PDB / ID: 3znz | ||||||
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Title | Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin | ||||||
Components |
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Keywords | HYDROLASE | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Keusekotten, K. / Elliott, P.R. / Glockner, L. / Kulathu, Y. / Wauer, T. / Krappmann, D. / Hofmann, K. / Komander, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: Otulin Antagonizes Lubac Signaling by Specifically Hydrolyzing met1-Linked Polyubiquitin. Authors: Keusekotten, K. / Elliott, P.R. / Glockner, L. / Fiil, B.K. / Damgaard, R.B. / Kulathu, Y. / Wauer, T. / Hospenthal, M.K. / Gyrd-Hansen, M. / Krappmann, D. / Hofmann, K. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3znz.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3znz.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3znz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/3znz ftp://data.pdbj.org/pub/pdb/validation_reports/zn/3znz | HTTPS FTP |
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-Related structure data
Related structure data | 3znvSC 3znxC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 31894.590 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 80-352 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLACI / References: UniProt: Q96BN8, ubiquitinyl hydrolase 1 | ||||
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#2: Protein | Mass: 17135.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLACI / References: UniProt: F5H265, UniProt: P0CG48*PLUS | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | CHAIN B: THE LAST THREE RESIDUES (RGG) ARE PART OF THE SECOND UBIQUITIN SEQUENCE. THE UNIPROT ENTRY ...CHAIN B: THE LAST THREE RESIDUES (RGG) ARE PART OF THE SECOND UBIQUITIN SEQUENCE. THE UNIPROT ENTRY REFERS TO A GENE PRODUCT OF UB WHICH IS CLEAVED WITHIN CELLS TO YIELD MONO UB (FIRST HALF OF THE SEQUENCE). THE AUTHORS ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 29, 2012 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.8 Å / Num. obs: 42974 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 27.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZNV Resolution: 1.9→42.802 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML Details: RESIDUES 93,94,153,160,187,197,222 FROM CHAIN A AND RESIDUES 48,63 FROM CHAIN B HAVE DISORDERED SIDE CHAINS AND WERE TRIMMED TO THE CORRESPONDING ELECTRON DENSITY.
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.949 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→42.802 Å
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Refine LS restraints |
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LS refinement shell |
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