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Yorodumi- PDB-7jvz: SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jvz | |||||||||
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Title | SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XFEL MONOCLINIC STRUCTURE | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / Hydrolase | |||||||||
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.5 Å | |||||||||
Authors | Schmidt, M. / Malla, T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: SARS CoV-2 MAIN PROTEASE 3CLpro, ROOM TEMPERATURE, DAMAGE FREE XFEL MONOCLINIC STRUCTURE Authors: Schmidt, M. / Malla, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jvz.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jvz.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jvz_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 7jvz_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 7jvz_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7jvz_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/7jvz ftp://data.pdbj.org/pub/pdb/validation_reports/jv/7jvz | HTTPS FTP |
-Related structure data
Related structure data | 6y2eS 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 (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.5 / Details: 12.5 % PEG 3350, 100 mmol/L bistris |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.26 Å |
Detector | Type: SLAC ePix10k / Detector: PIXEL / Date: Aug 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33 Å / Num. obs: 9428 / % possible obs: 100 % / Redundancy: 51 % / CC1/2: 0.94 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.3 Å / Num. unique obs: 505 / CC1/2: 0.18 / R split: 1.77 |
Serial crystallography measurement | Focal spot size: 1 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1 µJ / Pulse photon energy: 9.8 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Description: MESH / Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6y2e Resolution: 2.5→32.67 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 13.738 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.784 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→32.67 Å
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Refine LS restraints |
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