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Yorodumi- PDB-7c8u: The crystal structure of COVID-19 main protease in complex with GC376 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c8u | |||||||||
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Title | The crystal structure of COVID-19 main protease in complex with GC376 | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | 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 / 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: 2.35 Å | |||||||||
Authors | Luan, X. / Shang, W. / Wang, Y. / Yin, W. / Jiang, Y. / Feng, S. / Wang, Y. / Liu, M. / Zhou, R. / Zhang, Z. ...Luan, X. / Shang, W. / Wang, Y. / Yin, W. / Jiang, Y. / Feng, S. / Wang, Y. / Liu, M. / Zhou, R. / Zhang, Z. / Wang, F. / Cheng, W. / Gao, M. / Wang, H. / Wu, W. / Tian, R. / Tian, Z. / Jin, Y. / Jiang, H.W. / Zhang, L. / Xu, H.E. / Zhang, S. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: The crystal structure of COVID-19 main protease in complex with GC376 Authors: Zhang, S.Y. / Luan, X.D. / Wang, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c8u.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c8u.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 7c8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/7c8u ftp://data.pdbj.org/pub/pdb/validation_reports/c8/7c8u | HTTPS FTP |
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-Related structure data
Related structure data | 1q2wS 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: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GC376 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 |
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#2: Chemical | ChemComp-K36 / ( |
#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: 2.03 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Lithium chloride, 0.1M Hepes pH 7, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→48.57 Å / Num. obs: 11269 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 1109 / CC1/2: 0.889 / Rpim(I) all: 0.23 / Rrim(I) all: 0.418 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1q2w Resolution: 2.35→44.352 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.205 / Average fsc free: 0.8686 / Average fsc work: 0.897 / Cross valid method: NONE / ESU R: 0.792 / ESU R Free: 0.312 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: 40.478 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→44.352 Å
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Refine LS restraints |
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LS refinement shell |
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