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Yorodumi- PDB-7uj9: Room-temperature X-ray structure of monomeric SARS-CoV-2 main pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uj9 | ||||||
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Title | Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-199) | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE / cysteine protease / catalytic domain / viral enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kovalevsky, A. / Kneller, D.W. / Coates, L. | ||||||
Funding support | 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Autoprocessing and oxyanion loop reorganization upon GC373 and nirmatrelvir binding of monomeric SARS-CoV-2 main protease catalytic domain. Authors: Nashed, N.T. / Kneller, D.W. / Coates, L. / Ghirlando, R. / Aniana, A. / Kovalevsky, A. / Louis, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uj9.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uj9.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/7uj9 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/7uj9 | HTTPS FTP |
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-Related structure data
Related structure data | 7ujgC 7ujuC 7ukkC 2qcyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22978.133 Da / Num. of mol.: 2 / Fragment: catalytic domain (MPro1-199) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 18-21% PEG3350, 0.1 M Bis-Tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→53.34 Å / Num. obs: 20094 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.952 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.05 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 2012 / CC1/2: 0.798 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCY Resolution: 2.25→28.7 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→28.7 Å
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Refine LS restraints |
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LS refinement shell |
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