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- PDB-7ofs: Structure of SARS-CoV-2 Papain-like protease PLpro in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ofs | |||||||||
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Title | Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 4-(2-hydroxyethyl)phenol | |||||||||
![]() | Papain-like protease nsp3 | |||||||||
![]() | HYDROLASE / Papain-like protease SARS-CoV-2 Hydrolase Zinc binding protein | |||||||||
Function / homology | ![]() viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Srinivasan, V. / Werner, N. / Falke, S. / Guenther, S. / Reinke, P. / Ewert, W. / Sprenger, J. / Koua, F. / Brognaro, H. / Ullah, N. ...Srinivasan, V. / Werner, N. / Falke, S. / Guenther, S. / Reinke, P. / Ewert, W. / Sprenger, J. / Koua, F. / Brognaro, H. / Ullah, N. / Andaleeb, H. / Perbandt, M. / Alves Franca, B. / Schwinzer, M. / Wang, M. / Lieske, J. / Ginn, H. / Lane, T.J. / Yefanov, O. / Gelisio, L. / Hakanpaeae, J. / Saouane, S. / Tolstikova, A. / Groessler, M. / Fleckenstein, H. / Trost, F. / Wolf, M. / Lorenzen, K. / Schubert, R. / Han, H. / Schmidt, C. / Brings, L. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Perk, A. / Awel, S. / Wahab, A. / Choudary, I. / Turk, D. / Hinrichs, W. / Chapman, H.N. / Meents, A. / Betzel, C. | |||||||||
Funding support | European Union, 2items
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![]() | ![]() Title: Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, ...Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, N. / Andaleeb, H. / Ullah, N. / Franca, B.A. / Wang, M. / Barra, A.L.C. / Perbandt, M. / Schwinzer, M. / Schmidt, C. / Brings, L. / Lorenzen, K. / Schubert, R. / Machado, R.R.G. / Candido, E.D. / Oliveira, D.B.L. / Durigon, E.L. / Niebling, S. / Garcia, A.S. / Yefanov, O. / Lieske, J. / Gelisio, L. / Domaracky, M. / Middendorf, P. / Groessler, M. / Trost, F. / Galchenkova, M. / Mashhour, A.R. / Saouane, S. / Hakanpaa, J. / Wolf, M. / Alai, M.G. / Turk, D. / Pearson, A.R. / Chapman, H.N. / Hinrichs, W. / Wrenger, C. / Meents, A. / Betzel, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.3 KB | Display | ![]() |
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PDB format | ![]() | 118.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 924 KB | Display | ![]() |
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Full document | ![]() | 928.4 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nfvSC ![]() 7oftC ![]() 7ofuC S: Starting model for refinement C: citing same article ( |
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Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35671.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Non-polymers , 6 types, 212 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/YRL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/YRL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-YRL / | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir ...Details: Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum. |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.78 Å / Num. obs: 42250 / % possible obs: 99.92 % / Redundancy: 11 % / Biso Wilson estimate: 43.69 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 10.5 % / Num. unique obs: 4154 / CC1/2: 0.505 / CC star: 0.819 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NFV Resolution: 1.9→44.78 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
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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 max: 137.65 Å2 / Biso mean: 51.785 Å2 / Biso min: 30.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→44.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 37.1827 Å / Origin y: 9.7339 Å / Origin z: 16.5612 Å
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Refinement TLS group | Selection details: (chain A and resseq 1:705) |