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Yorodumi- PDB-6y84: SARS-CoV-2 main protease with unliganded active site (2019-nCoV, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y84 | ||||||
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Title | SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19) | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / protease / cysteine protease | ||||||
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 / TRAF3-dependent IRF activation pathway / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 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 / molecular replacement / Resolution: 1.39 Å | ||||||
Authors | Owen, C.D. / Lukacik, P. / Strain-Damerell, C.M. / Douangamath, A. / Powell, A.J. / Fearon, D. / Brandao-Neto, J. / Crawshaw, A.D. / Aragao, D. / Williams, M. ...Owen, C.D. / Lukacik, P. / Strain-Damerell, C.M. / Douangamath, A. / Powell, A.J. / Fearon, D. / Brandao-Neto, J. / Crawshaw, A.D. / Aragao, D. / Williams, M. / Flaig, R. / Hall, D.R. / McAuley, K.E. / Mazzorana, M. / Stuart, D.I. / von Delft, F. / Walsh, M.A. | ||||||
Citation | Journal: To Be Published Title: COVID-19 main protease with unliganded active site Authors: Owen, C.D. / Lukacik, P. / Strain-Damerell, C.M. / Douangamath, A. / Powell, A.J. / Fearon, D. / Brandao-Neto, J. / Crawshaw, A.D. / Aragao, D. / Williams, M. / Flaig, R. / Hall, D. / ...Authors: Owen, C.D. / Lukacik, P. / Strain-Damerell, C.M. / Douangamath, A. / Powell, A.J. / Fearon, D. / Brandao-Neto, J. / Crawshaw, A.D. / Aragao, D. / Williams, M. / Flaig, R. / Hall, D. / McAauley, K. / Stuart, D.I. / von Delft, F. / Walsh, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y84.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y84.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y84 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y84 | HTTPS FTP |
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-Related structure data
Related structure data | 6yb7C 6lu7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 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, SARS coronavirus main proteinase | ||||
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#2: Chemical | ChemComp-DMS / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% PEG 4000, 5% DMSO, 0.1M MES pH 6.5. 0.15 microlitre protein + 0.3 microlitre reservoir + 0.05 microlitre seed stock |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9126 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.39→54.93 Å / Num. obs: 50348 / % possible obs: 97.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Rrim(I) all: 0.069 / Net I/σ(I): 9.7 / Num. measured all: 179937 / Scaling rejects: 602 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.468
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 1.39→54.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.068
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Displacement parameters | Biso max: 97.94 Å2 / Biso mean: 21 Å2 / Biso min: 10.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.39→54.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 11.7561 Å / Origin y: 0.8392 Å / Origin z: 4.6891 Å
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Refinement TLS group | Selection details: { A|* } |