- PDB-4hxd: Diversity of ubiquitin and ISG15 specificity amongst nairoviruses... -
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Basic information
Entry
Database: PDB / ID: 4hxd
Title
Diversity of ubiquitin and ISG15 specificity amongst nairoviruses viral ovarian tumor domain proteases
Components
Polyubiquitin-C
RNA-directed RNA polymerase L
Keywords
hydrolase/viral protein / OTU-like Cysteine protease / Dugbe virus / deubiquitinase / 3-AMINOPROPANE / ubiquitin hydrolase / viral protein / hydrolase / ubiquitin. / hydrolase-viral protein complex
Function / homology
Function and homology information
cysteine-type deubiquitinase activity => GO:0004843 / RNA-templated viral transcription / negative stranded viral RNA replication / 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 ...cysteine-type deubiquitinase activity => GO:0004843 / RNA-templated viral transcription / negative stranded viral RNA replication / 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 / 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 / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / 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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / 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 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of FGFR1 signaling Similarity search - Function
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger C2H2 type domain signature. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology
Mass: 8519.778 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pTyB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: P0CG48, ubiquitinyl hydrolase 1
#2: Protein
RNA-directedRNApolymeraseL / Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thioesterase / RNA- ...Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thioesterase / RNA-directed RNA polymerase
Mass: 20011.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dugbe virus (isolate ArD44313) / Gene: L / Plasmid: pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q66431, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
3-AMINOPROPANE WAS COVALENTLY ADDED TO THE C-TERMINUS OF UBIQUITIN THROUGH USE OF INTERN CHEMISTRY ...3-AMINOPROPANE WAS COVALENTLY ADDED TO THE C-TERMINUS OF UBIQUITIN THROUGH USE OF INTERN CHEMISTRY BY COMPLEXING THE THIOESTERIFIED UBIQUITIN PROTEIN TOGETHER WITH 3-BROMOPROPYLAMINE AS PER WILKINSON, K. D., T. GAN-ERDENE, AND N. KOLLI. 2005. DERIVITIZATION OF THE C-TERMINUS OF UBIQUITIN AND UBIQUITIN-LIKE PROTEINS USING INTEIN CHEMISTRY: METHODS AND USES. METHODS ENZYMOL 399:37-51.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.25 M LiSO4, 0.10 M Bis-Tris, 29% PEG 3350, 40% (v/v) 1,3-butanediol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector
Type: NOIR-1 / Detector: CCD / Date: Apr 4, 2012
Radiation
Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
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