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Yorodumi- PDB-6wtt: Crystals Structure of the SARS-CoV-2 (COVID-19) main protease wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wtt | |||||||||
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Title | Crystals Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor GC-376 | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / COVID COVID19 COVID-19 SARS SARS COV2 COV NCOV 19 CORONAVIRUS MAIN PROTEASE 3CL MPRO PRO / GC376 / GC-376 / PEPTIDOMIMETIC / PROTEASE / CYSTEINE | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.15 Å | |||||||||
Authors | Sacco, M. / Ma, C. / Chen, Y. / Wang, J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Res. / Year: 2020 Title: Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Authors: Ma, C. / Sacco, M.D. / Hurst, B. / Townsend, J.A. / Hu, Y. / Szeto, T. / Zhang, X. / Tarbet, B. / Marty, M.T. / Chen, Y. / Wang, J. #1: Journal: Biorxiv / Year: 2020 Title: Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Authors: Ma, C. / Sacco, M.D. / Hurst, B. / Townsend, J.A. / Hu, Y. / Szeto, T. / Zhang, X. / Tarbet, B. / Marty, M.T. / Chen, Y. / Wang, J. #2: Journal: Cell Res. / Year: 2020 Title: Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Authors: Ma, C. / Sacco, M.D. / Hurst, B. / Townsend, J.A. / Hu, Y. / Szeto, T. / Zhang, X. / Tarbet, B. / Marty, M.T. / Chen, Y. / Wang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wtt.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wtt.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wtt ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wtt | HTTPS FTP |
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-Related structure data
Related structure data | 5rggS 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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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 34379.117 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: GC-376 Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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-Non-polymers , 7 types, 339 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-B1S / ( | #8: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 2k, 10 % 1,6-HexD, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 52883 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.037 / Rrim(I) all: 0.116 / Χ2: 1.006 / Net I/σ(I): 5.2 / Num. measured all: 499786 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5rgg Resolution: 2.15→48.56 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.285 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 160.09 Å2 / Biso mean: 61.119 Å2 / Biso min: 22.71 Å2
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Refinement step | Cycle: final / Resolution: 2.15→48.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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