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Yorodumi- PDB-7nt4: X-ray structure of SCoV2-PLpro in complex with small molecule inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nt4 | ||||||
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Title | X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | HYDROLASE / Drug repurposing / SCoV2-PLpro inhibitor | ||||||
Function / homology | Function and homology information 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 ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / 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 / 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 / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Napolitano, V. / Mourao, A. / Bostock, M. / Matsuda, A. / Czarna, A. / Popowicz, G.M. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2022 Title: Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses. Authors: Napolitano, V. / Dabrowska, A. / Schorpp, K. / Mourao, A. / Barreto-Duran, E. / Benedyk, M. / Botwina, P. / Brandner, S. / Bostock, M. / Chykunova, Y. / Czarna, A. / Dubin, G. / Frohlich, T. ...Authors: Napolitano, V. / Dabrowska, A. / Schorpp, K. / Mourao, A. / Barreto-Duran, E. / Benedyk, M. / Botwina, P. / Brandner, S. / Bostock, M. / Chykunova, Y. / Czarna, A. / Dubin, G. / Frohlich, T. / Holscher, M. / Jedrysik, M. / Matsuda, A. / Owczarek, K. / Pachota, M. / Plettenburg, O. / Potempa, J. / Rothenaigner, I. / Schlauderer, F. / Slysz, K. / Szczepanski, A. / Greve-Isdahl Mohn, K. / Blomberg, B. / Sattler, M. / Hadian, K. / Popowicz, G.M. / Pyrc, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nt4.cif.gz | 265.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nt4.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/7nt4 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/7nt4 | HTTPS FTP |
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-Related structure data
Related structure data | 6w9cS S: Starting model for refinement |
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Similar 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 9 - 315 / Label seq-ID: 11 - 317
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35930.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Non-polymers , 5 types, 213 molecules
#2: Chemical | ChemComp-PRL / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.45 Å3/Da / Density % sol: 64.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.05 M Sodium cacodylate pH 6.5 0.2 M Potassium chloride, 0.1 M Magnesium acetate 10 %(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.678→49.47 Å / Num. obs: 21442 / % possible obs: 95.7 % / Redundancy: 38.1 % / CC1/2: 0.99 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.678→2.969 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1073 / CC1/2: 0.699 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W9C Resolution: 2.68→49.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.868 / SU B: 27.963 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.23 Å2 / Biso mean: 42.655 Å2 / Biso min: 2.96 Å2
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Refinement step | Cycle: final / Resolution: 2.68→49.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9139 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.68→2.748 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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