+Open data
-Basic information
Entry | Database: PDB / ID: 9epm | ||||||
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Title | Mpro from SARS-CoV-2 with 4A mutation | ||||||
Components | Non-structural protein 11 | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / main protease / oligomerization | ||||||
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: 1.981 Å | ||||||
Authors | Plewka, J. / Lis, K. / Czarna, A. / Pyrc, K. / Kantyka, T. / Chykunova, Y. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: SARS-CoV-2 M pro oligomerization as a potential target for therapy. Authors: Lis, K. / Plewka, J. / Menezes, F. / Bielecka, E. / Chykunova, Y. / Pustelny, K. / Niebling, S. / Garcia, A.S. / Garcia-Alai, M. / Popowicz, G.M. / Czarna, A. / Kantyka, T. / Pyrc, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9epm.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9epm.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 9epm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/9epm ftp://data.pdbj.org/pub/pdb/validation_reports/ep/9epm | HTTPS FTP |
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-Related structure data
Related structure data | 9eplC 9eurC 9eusC 9ewmC 9ewnC 9ewoC 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
#1: Protein | Mass: 33119.770 Da / Num. of mol.: 1 / Mutation: R4A 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 |
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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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% Polyethylene glycol monomethyl ether 5.000, 200 mM Potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→48.125 Å / Num. obs: 18323 / % possible obs: 98.6 % / Redundancy: 6.3 % / CC1/2: 0.967 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 1.98→2.08 Å / Num. unique obs: 1210 / CC1/2: 0.346 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→48.125 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.374 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.199 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.564 Å2
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Refinement step | Cycle: LAST / Resolution: 1.981→48.125 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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