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Open data
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Basic information
Entry | Database: PDB / ID: 6yva | |||||||||
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Title | PLpro-C111S with mISG15 | |||||||||
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![]() | CELL INVASION / Deubiquitinase / papain-like-protease / SARS-CoV-2 / ISG15 / complex | |||||||||
Function / homology | ![]() positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / 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 / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / 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 / viral genome replication / positive regulation of erythrocyte differentiation / methyltransferase activity / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / protein tag activity / positive regulation of type II interferon production / integrin binding / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / methylation / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / defense response to bacterium / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shin, D. / Dikic, I. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van ...Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van Noort, G.J. / Ovaa, H. / Muller, S. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I. #1: ![]() Title: Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / ...Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / Ovaa, H. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.8 KB | Display | ![]() |
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PDB format | ![]() | 151 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 35655.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, UniProt: P0DTD1*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase |
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#2: Protein | Mass: 17919.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG4450, 100 mM bis-tris propane pH 6.5, 200 mM Potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→45.34 Å / Num. obs: 10590 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 88.46 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05751 / Net I/σ(I): 8.58 |
Reflection shell | Resolution: 3.185→3.298 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5689 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1008 / CC1/2: 0.594 / CC star: 0.863 / % possible all: 97.77 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6W9C, 5TLA Resolution: 3.18→45.34 Å / SU ML: 0.5141 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5098 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: 87.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.18→45.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 38.6251045464 Å / Origin y: -33.7660531 Å / Origin z: 2.62099956023 Å
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Refinement TLS group | Selection details: all |