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Yorodumi- PDB-6xbi: Crystal structure of the SARS-CoV-2 (COVID-19) main protease in c... -
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-Basic information
Entry | Database: PDB / ID: 6xbi | |||||||||
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Title | Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor UAW248 | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / COVID / COVID19 / COVID-19 / SARS / SARS COV2 / COV / NCOV 19 / CORONAVIRUS / MAIN PROTEASE / 3CL / MPRO / PRO / VIRAL PROTEIN / GC376 / calpain inhibitor II / leupeptin / calpain / aldehyde / GC-376 / 3cl-like / a-ketoamide / UAW41 / UAW246 / UAW247 / UAW248 / 246 / 247 / 248 / alpheketoamide / alpha / ketoamide / PEPTIDOMIMETIC / PROTEASE / CYSTEINE / HYDROLASE-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 / 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 / 3'-5'-RNA exonuclease activity / 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 / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Sacco, M. / Ma, C. / Wang, J. / Chen, Y. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L. Authors: Sacco, M.D. / Ma, C. / Lagarias, P. / Gao, A. / Townsend, J.A. / Meng, X. / Dube, P. / Zhang, X. / Hu, Y. / Kitamura, N. / Hurst, B. / Tarbet, B. / Marty, M.T. / Kolocouris, A. / Xiang, Y. / 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 | 6xbi.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xbi.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xbi_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 6xbi_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 6xbi_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 6xbi_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xbi ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xbi | HTTPS FTP |
-Related structure data
Related structure data | 6xa4C 6xbgC 6xbhC 6xfnC 6yb7S 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
-Protein / Protein/peptide , 2 types, 4 molecules ABDE
#1: Protein | Mass: 34094.887 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3569 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: Protein/peptide | |
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-Non-polymers , 4 types, 378 molecules
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-DMS / | #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: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 20% PEG3000, 0.1 M sodium citrate, pH 5.6 |
-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: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2020 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 58337 / % possible obs: 85.2 % / Redundancy: 2.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.99 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 4573 / CC1/2: 0.627 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6YB7 Resolution: 1.7→47.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.71 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.126 / 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: 80.45 Å2 / Biso mean: 26.328 Å2 / Biso min: 9.03 Å2
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Refinement step | Cycle: final / Resolution: 1.7→47.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.746 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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