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Yorodumi- PDB-7owd: Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal spac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7owd | |||||||||
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Title | Structure of CYLD CAP-Gly3 (467-552) bound to Ub; tetragonal space group | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / ubiquitin binding domain / deubiquitinating enzyme | |||||||||
Function / homology | Function and homology information negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip ...negative regulation of interleukin-18-mediated signaling pathway / Met1-linked polyubiquitin deubiquitinase activity / protein linear deubiquitination / ripoptosome assembly involved in necroptotic process / regulation of intrinsic apoptotic signaling pathway / regulation of B cell differentiation / : / regulation of cilium assembly / negative regulation of p38MAPK cascade / ciliary tip / regulation of necroptotic process / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of JNK cascade / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / proline-rich region binding / negative regulation of non-canonical NF-kappaB signal transduction / K48-linked deubiquitinase activity / TNFR1-induced proapoptotic signaling / positive regulation of T cell differentiation / negative regulation of type I interferon production / K63-linked deubiquitinase activity / positive regulation of protein localization / positive regulation of T cell receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / necroptotic process / homeostasis of number of cells / regulation of microtubule cytoskeleton organization / 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 / regulation of mitotic cell cycle / 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) / ciliary basal body / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Elliott, P.R. / Komander, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell Rep / Year: 2021 Title: Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains. Authors: Elliott, P.R. / Leske, D. / Wagstaff, J. / Schlicher, L. / Berridge, G. / Maslen, S. / Timmermann, F. / Ma, B. / Fischer, R. / Freund, S.M.V. / Komander, D. / Gyrd-Hansen, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7owd.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7owd.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 7owd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owd ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owd | HTTPS FTP |
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-Related structure data
Related structure data | 7owcC 1ixdS 1ubqS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9384.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYLD, CYLD1, KIAA0849, HSPC057 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NQC7, ubiquitinyl hydrolase 1 |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / 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: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 40 (v/v) PEG 300, 100 mM phosphate/citrate pH 4.2 |
-Data collection
Diffraction | Mean temperature: 210 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→41.64 Å / Num. obs: 18356 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.71→1.74 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 933 / CC1/2: 0.899 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UBQ, 1IXD Resolution: 1.71→41.64 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 34.1202 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→41.64 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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