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Yorodumi- PDB-4ium: Equine arteritis virus papain-like protease 2 (PLP2) covalently b... -
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-Basic information
Entry | Database: PDB / ID: 4ium | ||||||
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Title | Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / viral ovarian tumor domain (OTU) protease / deubiquitinase / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease 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 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / 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 / Peroxisomal protein import / Termination of translesion DNA synthesis / 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 / EGFR downregulation / Negative regulation of FGFR1 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport Similarity search - Function | ||||||
Biological species | Equine arteritis virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å | ||||||
Authors | Bailey-Elkin, B.A. / James, T.W. / Mark, B.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. Authors: van Kasteren, P.B. / Bailey-Elkin, B.A. / James, T.W. / Ninaber, D.K. / Beugeling, C. / Khajehpour, M. / Snijder, E.J. / Mark, B.L. / Kikkert, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ium.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ium.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ium.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4ium ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4ium | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15234.333 Da / Num. of mol.: 1 / Fragment: UNP residues 261-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equine arteritis virus / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Protein | Mass: 8560.874 Da / Num. of mol.: 1 / Fragment: UNP residues 1-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 100 mM MES, pH 6.2, 18% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28243, 1.28289, 1.27347 | ||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 29, 2011 Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, uncoated, and Pd strips | ||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.45→31.11 Å / Num. all: 36356 / Num. obs: 36344 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.5 / Redundancy: 8.7 % / Rmerge(I) obs: 0.049 | ||||||||||||
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 7.1 / Num. unique all: 5029 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→31.02 Å / SU ML: 0.26 / σ(F): 1.05 / Phase error: 17.33 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.83 Å2 / ksol: 0.413 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.45→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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