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Yorodumi- PDB-8dk8: Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dk8 | |||||||||
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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 | HYDROLASE / viral protein / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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: 2.6 Å | |||||||||
Authors | Khan, M.B. / Lu, J. / 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 M pro 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 | 8dk8.cif.gz | 297.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dk8.ent.gz | 201.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/8dk8 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/8dk8 | HTTPS FTP |
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-Related structure data
Related structure data | 8djjC 8dkzC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.999999872095, -0.000442725297694, -0.000244548326013), (-0.000443138000824, 0.999998473517, 0.00169014554187), (0.000243799682526, 0.00169025369435, -0.999998541801) ...NCS oper: (Code: given Matrix: (-0.999999872095, -0.000442725297694, -0.000244548326013), Vector: |
-Components
#1: Protein | Mass: 33837.602 Da / Num. of mol.: 2 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 #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 Å3/Da / Density % sol: 38.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging 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: CLSI / Beamline: 08B1-1 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.85 Å / Num. obs: 52297 / % possible obs: 93.92 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.69 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 2.6→2.69 Å / Num. unique obs: 15199 / CC1/2: 0.752 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WTM Resolution: 2.6→43.85 Å / SU ML: 0.4372 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.3156 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: 56.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→43.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.737682200033 Å | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.96903842543 Å / Origin y: -16.1551169419 Å / Origin z: 26.5103414905 Å
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Refinement TLS group | Selection details: all |