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Yorodumi- PDB-7uju: Room-temperature X-ray structure of monomeric SARS-CoV-2 main pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uju | ||||||
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Title | Room-temperature X-ray structure of monomeric SARS-CoV-2 main protease catalytic domain (MPro1-196) in complex with nirmatrelvir | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE/INHIBITOR / cysteine protease / catalytic domain / viral enzyme / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
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 / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...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 / 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 / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / 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: 1.85 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 | 7uju.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uju.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 7uju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uju_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7uju_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7uju_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7uju_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/7uju ftp://data.pdbj.org/pub/pdb/validation_reports/uj/7uju | HTTPS FTP |
-Related structure data
Related structure data | 7uj9C 7ujgC 7ukkC 2qcyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21646.734 Da / Num. of mol.: 2 / Fragment: catalytic domain (MPro1-196) 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: 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: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 287 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: Dec 7, 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: 1.85→62.6 Å / Num. obs: 32399 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.32 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 3115 / CC1/2: 0.65 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qcy Resolution: 1.85→26.03 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74 / 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: 1.85→26.03 Å
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Refine LS restraints |
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LS refinement shell |
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