+Open data
-Basic information
Entry | Database: PDB / ID: 7dat | ||||||
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Title | The crystal structure of COVID-19 main protease treated by AF | ||||||
Components | COVID-19 MAIN PROTEASE | ||||||
Keywords | VIRAL PROTEIN / PROTEASE | ||||||
Function / homology | Function and homology information viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / methylation / double membrane vesicle viral factory outer membrane ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / 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 / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | He, Z.S. / He, B. / Cao, P. / Jiang, H.D. / Gong, Y. / Gao, X.Y. | ||||||
Citation | Journal: Nano Today / Year: 2022 Title: A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster. Authors: He, Z. / Ye, F. / Zhang, C. / Fan, J. / Du, Z. / Zhao, W. / Yuan, Q. / Niu, W. / Gao, F. / He, B. / Cao, P. / Zhao, L. / Gao, X. / Gao, X. / Sun, B. / Dong, Y. / Zhao, J. / Qi, J. / Liang, X. ...Authors: He, Z. / Ye, F. / Zhang, C. / Fan, J. / Du, Z. / Zhao, W. / Yuan, Q. / Niu, W. / Gao, F. / He, B. / Cao, P. / Zhao, L. / Gao, X. / Gao, X. / Sun, B. / Dong, Y. / Zhao, J. / Qi, J. / Liang, X.J. / Jiang, H. / Gong, Y. / Tan, W. / Gao, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dat.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dat.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7dat ftp://data.pdbj.org/pub/pdb/validation_reports/da/7dat | HTTPS FTP |
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-Related structure data
Related structure data | 7dauC 7davC 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.: 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: P0DTC1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase | ||||
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#2: Chemical | #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: 38.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200mM KF and 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.86 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 6797 / % possible obs: 96.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.88 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.75→2.9 Å / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 7 / Num. unique obs: 823 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 2.75→31.45 Å / SU ML: 0.2556 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4327 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.77 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→31.45 Å
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Refine LS restraints |
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LS refinement shell |
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