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Yorodumi- PDB-7ddc: Crystal structure of SARS-CoV-2 main protease in complex with Taf... -
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-Basic information
Entry | Database: PDB / ID: 7ddc | |||||||||
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Title | Crystal structure of SARS-CoV-2 main protease in complex with Tafenoquine | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / main protease / 3C-like proteinase | |||||||||
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 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.175 Å | |||||||||
Authors | Chen, Y. / Wang, Y.C. / Yang, C.S. / Hung, M.C. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Tafenoquine and its derivatives as inhibitors for the severe acute respiratory syndrome coronavirus 2. Authors: Chen, Y. / Yang, W.H. / Chen, H.F. / Huang, L.M. / Gao, J.Y. / Lin, C.W. / Wang, Y.C. / Yang, C.S. / Liu, Y.L. / Hou, M.H. / Tsai, C.L. / Chou, Y.Z. / Huang, B.Y. / Hung, C.F. / Hung, Y.L. / ...Authors: Chen, Y. / Yang, W.H. / Chen, H.F. / Huang, L.M. / Gao, J.Y. / Lin, C.W. / Wang, Y.C. / Yang, C.S. / Liu, Y.L. / Hou, M.H. / Tsai, C.L. / Chou, Y.Z. / Huang, B.Y. / Hung, C.F. / Hung, Y.L. / Wang, W.J. / Su, W.C. / Kumar, V. / Wu, Y.C. / Chao, S.W. / Chang, C.S. / Chen, J.S. / Chiang, Y.P. / Cho, D.Y. / Jeng, L.B. / Tsai, C.H. / Hung, M.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ddc.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ddc.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ddc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ddc_validation.pdf.gz | 809.7 KB | Display | wwPDB validaton report |
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Full document | 7ddc_full_validation.pdf.gz | 813.8 KB | Display | |
Data in XML | 7ddc_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7ddc_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/7ddc ftp://data.pdbj.org/pub/pdb/validation_reports/dd/7ddc | HTTPS FTP |
-Related structure data
Related structure data | 6lu7S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33882.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-H3F / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium acetate,0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.175→27.586 Å / Num. obs: 14115 / % possible obs: 99.62 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.382 |
Reflection shell | Resolution: 2.175→2.253 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.234 / Num. unique obs: 1369 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 2.175→27.586 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.617 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.324 / ESU R Free: 0.22 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.516 Å2
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Refinement step | Cycle: LAST / Resolution: 2.175→27.586 Å
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Refine LS restraints |
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LS refinement shell |
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