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Yorodumi- PDB-8ddi: Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166N Mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ddi | ||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166N Mutant | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / Protease / SARS-CoV-2 / Mpro / Mutation | ||||||
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: 2.8 Å | ||||||
Authors | Lewandowski, E.M. / Jacobs, L.M.C. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2023 Title: A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. Authors: Ou, J. / Lewandowski, E.M. / Hu, Y. / Lipinski, A.A. / Aljasser, A. / Colon-Ascanio, M. / Morgan, R.T. / Jacobs, L.M.C. / Zhang, X. / Bikowitz, M.J. / Langlais, P.R. / Tan, H. / Wang, J. / Chen, Y. / Choy, J.S. #1: Journal: Biorxiv / Year: 2022 Title: A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations. Authors: Ou, J. / Lewandowski, E.M. / Hu, Y. / Lipinski, A.A. / Morgan, R.T. / Jacobs, L.M.C. / Zhang, X. / Bikowitz, M.J. / Langlais, P. / Tan, H. / Wang, J. / Chen, Y. / Choy, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ddi.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ddi.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ddi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/8ddi ftp://data.pdbj.org/pub/pdb/validation_reports/dd/8ddi | HTTPS FTP |
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-Related structure data
Related structure data | 8ddmC 7lyhS 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: 33810.535 Da / Num. of mol.: 1 / Mutation: E166N 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: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Magnesium Chloride, 20% PEG 3350, 10% 1-6HexD, 0.1M HEPES pH 7.5, 0.1M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 6641 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 277 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LYH Resolution: 2.8→43.81 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.891 / SU B: 39.332 / SU ML: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 101.9 Å2 / Biso mean: 47.219 Å2 / Biso min: 23.47 Å2
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Refinement step | Cycle: final / Resolution: 2.8→43.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 12.3762 Å / Origin y: -0.1753 Å / Origin z: 4.1438 Å
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