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Yorodumi- PDB-3phx: OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3phx | ||||||
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Title | OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15 | ||||||
Components |
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Keywords | Hydrolase/Protein Binding / OTU domain / De-ubiquitinase / De-ISGylase / Hydrolase-Protein Binding complex | ||||||
Function / homology | Function and homology information positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / RNA-templated viral transcription / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / negative stranded viral RNA replication / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication ...positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / RNA-templated viral transcription / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / negative stranded viral RNA replication / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / Negative regulators of DDX58/IFIH1 signaling / integrin-mediated signaling pathway / Termination of translesion DNA synthesis / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / modification-dependent protein catabolic process / PKR-mediated signaling / ISG15 antiviral mechanism / protein tag activity / Interferon alpha/beta signaling / positive regulation of type II interferon production / integrin binding / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / defense response to bacterium / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / innate immune response / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Crimean-Congo hemorrhagic fever virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Akutsu, M. / Ye, Y. / Virdee, S. / Komander, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains. Authors: Akutsu, M. / Ye, Y. / Virdee, S. / Chin, J.W. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3phx.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phx.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 3phx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phx ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phx | HTTPS FTP |
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-Related 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21011.580 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: Nigeria/IbAr10200/1970 / Gene: L / Production host: Escherichia coli (E. coli) References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase |
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#2: Protein | Mass: 8985.266 Da / Num. of mol.: 1 / Fragment: UNP residues 79-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161 |
-Non-polymers , 4 types, 207 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-NEH / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG8K, 0.2M zinc acetate, 0.1M MES sodium salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2010 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 33549 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.659 Å2 / ksol: 0.438 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell |
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