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Yorodumi- PDB-6wnp: X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wnp | ||||||
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Title | X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Covid-19 / main protease / 3CL-protease / Boceprevir / FDA Drug / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
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 / Resolution: 1.443 Å | ||||||
Authors | Anson, B. / Mesecar, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: X-ray Structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 A Authors: Anson, B. / Mesecar, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wnp.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wnp.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/6wnp ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wnp | HTTPS FTP |
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-Related structure data
Related structure data | 6w63S 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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Unit cell |
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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 BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-U5G / |
#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: 2.85 Å3/Da / Density % sol: 56.81 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.67 mM DTT, 0.33% MPD, 16.7 mM MES pH 6.0, 26.7 mM KCl, 5% PEG-10,000, 16.7 mM HEPES pH 7.5, 0.67% DMSO and 200 uM Boceprevir |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2020 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→25.823 Å / Num. obs: 67447 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.04 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06428 / Rpim(I) all: 0.03383 / Rrim(I) all: 0.07286 / Net I/σ(I): 19.85 |
Reflection shell | Resolution: 1.443→1.494 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5341 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 6435 / CC1/2: 0.926 / CC star: 0.981 / Rpim(I) all: 0.2782 / Rrim(I) all: 0.6036 / % possible all: 95.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W63 Resolution: 1.443→25.81 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3267
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.443→25.81 Å
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Refine LS restraints |
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LS refinement shell |
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