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Yorodumi- PDB-8di3: Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8di3 | |||||||||
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Title | Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates | |||||||||
Components | 3C-like proteinase nsp5 | |||||||||
Keywords | VIRAL PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex / 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 / 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: 1.5 Å | |||||||||
Authors | Lu, J. / Khan, M.B. / Young, H.S. / Lemieux, M.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: SARS-CoV-2 Mpro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals Authors: Chen, S.A. / Arutyunova, E. / Lu, J. / Khan, M.B. / Rut, W. / Zmudzinski, M. / Shahbaz, S. / Iyyathurai, J. / Moussa, E.W. / Turner, Z. / Bai, B. / Lamer, T. / Nieman, J.A. / Vederas, J.C. / ...Authors: Chen, S.A. / Arutyunova, E. / Lu, J. / Khan, M.B. / Rut, W. / Zmudzinski, M. / Shahbaz, S. / Iyyathurai, J. / Moussa, E.W. / Turner, Z. / Bai, B. / Lamer, T. / Nieman, J.A. / Vederas, J.C. / Julien, O. / Drag, M. / Elahi, S. / Young, H.S. / Lemieux, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8di3.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8di3.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 8di3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8di3 ftp://data.pdbj.org/pub/pdb/validation_reports/di/8di3 | HTTPS FTP |
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-Related structure data
Related structure data | 8dkhC 8dkjC 8dkkC 8dklC 8dmnC 8ej7C 8ej9C 6wtmS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33866.578 Da / Num. of mol.: 1 / Mutation: P132H 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 |
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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: 1.94 Å3/Da / Density % sol: 36.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Phosphate, 0.1 M Tris, 50 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.09 Å / Num. obs: 79605 / % possible obs: 98.01 % / Redundancy: 5.4 % / Biso Wilson estimate: 21.25 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 11.03 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 40798 / CC1/2: 0.997 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WTM Resolution: 1.5→31.09 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 26.9117 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: 28.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→31.09 Å
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Refine LS restraints |
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LS refinement shell |
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