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Yorodumi- PDB-7com: Crystal structure of the SARS-CoV-2 main protease in complex with... -
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-Basic information
Entry | Database: PDB / ID: 7com | ||||||
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Title | Crystal structure of the SARS-CoV-2 main protease in complex with Boceprevir (space group P212121) | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / coronavirus / protease / inhibitor / complex / viral protein. | ||||||
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: 2.25 Å | ||||||
Authors | Zeng, R. / Qiao, J.X. / Wang, Y.F. / Li, Y.S. / Yao, R. / Liu, J.M. / Zhou, Y.L. / Chen, P. / Yang, S.Y. / Lei, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Science / Year: 2021 Title: SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Authors: Qiao, J. / Li, Y.S. / Zeng, R. / Liu, F.L. / Luo, R.H. / Huang, C. / Wang, Y.F. / Zhang, J. / Quan, B. / Shen, C. / Mao, X. / Liu, X. / Sun, W. / Yang, W. / Ni, X. / Wang, K. / Xu, L. / ...Authors: Qiao, J. / Li, Y.S. / Zeng, R. / Liu, F.L. / Luo, R.H. / Huang, C. / Wang, Y.F. / Zhang, J. / Quan, B. / Shen, C. / Mao, X. / Liu, X. / Sun, W. / Yang, W. / Ni, X. / Wang, K. / Xu, L. / Duan, Z.L. / Zou, Q.C. / Zhang, H.L. / Qu, W. / Long, Y.H. / Li, M.H. / Yang, R.C. / Liu, X. / You, J. / Zhou, Y. / Yao, R. / Li, W.P. / Liu, J.M. / Chen, P. / Liu, Y. / Lin, G.F. / Yang, X. / Zou, J. / Li, L. / Hu, Y. / Lu, G.W. / Li, W.M. / Wei, Y.Q. / Zheng, Y.T. / Lei, J. / Yang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7com.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7com.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 7com.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7com_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7com_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7com_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 7com_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/7com ftp://data.pdbj.org/pub/pdb/validation_reports/co/7com | HTTPS FTP |
-Related structure data
Related structure data | 7c7pSC 7d3iC 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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 21% (v/v) PEG 4000; 20% (v/v) PEG400; 0.1 M MES pH6.5; |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.85 Å / Num. obs: 33972 / % possible obs: 99.9 % / Redundancy: 14.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.048 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.25→2.32 Å / Rmerge(I) obs: 1.423 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3097 / CC1/2: 0.83 / Rpim(I) all: 0.405 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C7P Resolution: 2.25→19.85 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.873 / SU R Cruickshank DPI: 0.275 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.215
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Displacement parameters | Biso mean: 40.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.27 Å
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