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Yorodumi- PDB-7rfr: Structure of SARS-CoV-2 main protease in complex with a covalent ... -
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-Basic information
Entry | Database: PDB / ID: 7rfr | ||||||
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Title | Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/INHIBITOR / Protease SARS-CoV-2 Covalent complex inhibitor / HYDROLASE-INHIBITOR complex | ||||||
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 / symbiont-mediated suppression of host NF-kappaB cascade / 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 / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 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 / 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 / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / 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: 1.626 Å | ||||||
Authors | Gajiwala, K.S. / Ferre, R.A. / Liu, W. / Stewart, A.E. | ||||||
Citation | Journal: Science / Year: 2021 Title: An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19. Authors: Owen, D.R. / Allerton, C.M.N. / Anderson, A.S. / Aschenbrenner, L. / Avery, M. / Berritt, S. / Boras, B. / Cardin, R.D. / Carlo, A. / Coffman, K.J. / Dantonio, A. / Di, L. / Eng, H. / Ferre, ...Authors: Owen, D.R. / Allerton, C.M.N. / Anderson, A.S. / Aschenbrenner, L. / Avery, M. / Berritt, S. / Boras, B. / Cardin, R.D. / Carlo, A. / Coffman, K.J. / Dantonio, A. / Di, L. / Eng, H. / Ferre, R. / Gajiwala, K.S. / Gibson, S.A. / Greasley, S.E. / Hurst, B.L. / Kadar, E.P. / Kalgutkar, A.S. / Lee, J.C. / Lee, J. / Liu, W. / Mason, S.W. / Noell, S. / Novak, J.J. / Obach, R.S. / Ogilvie, K. / Patel, N.C. / Pettersson, M. / Rai, D.K. / Reese, M.R. / Sammons, M.F. / Sathish, J.G. / Singh, R.S.P. / Steppan, C.M. / Stewart, A.E. / Tuttle, J.B. / Updyke, L. / Verhoest, P.R. / Wei, L. / Yang, Q. / Zhu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rfr.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rfr.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rfr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7rfr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7rfr_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 7rfr_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/7rfr ftp://data.pdbj.org/pub/pdb/validation_reports/rf/7rfr | HTTPS FTP |
-Related structure data
Related structure data | 7rfsC 7rfuC 7rfwC 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
#1: Protein | Mass: 33825.547 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, SARS coronavirus main proteinase #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: 0.1 M MES, pH 6.0, 20.0% w/v PEG6000, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.626→72.115 Å / Num. obs: 59000 / % possible obs: 65.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.626→1.732 Å / Num. unique obs: 2951 / CC1/2: 0.564 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6LU7 Resolution: 1.626→72.11 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.128
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Displacement parameters | Biso mean: 25.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.626→72.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.69 Å
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