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Yorodumi- PDB-8cac: Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with... -
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-Basic information
Entry | Database: PDB / ID: 8cac | ||||||
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Title | Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | ANTIVIRAL PROTEIN / Mpro mutations main protease SARS-CoV-2 | ||||||
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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Ibrahim, M. / El Kilani, H. / Hilgenfeld, R. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K Authors: Ibrahim, M. / El Kilani, H. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cac.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cac.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cac_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cac_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cac_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 8cac_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/8cac ftp://data.pdbj.org/pub/pdb/validation_reports/ca/8cac | HTTPS FTP |
-Related structure data
Related structure data | 6y2eS 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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Unit cell |
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-Components
#1: Protein | Mass: 33375.043 Da / Num. of mol.: 2 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: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | 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: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Bis-Tris, Potassium citrate tribasic monohydrate, PEG 3350, Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.003 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→46.061 Å / Num. obs: 40658 / % possible obs: 99.81 % / Redundancy: 7.5 % / Biso Wilson estimate: 42.05 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 9.71 |
Reflection shell | Resolution: 2.15→2.23 Å / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3883 / CC1/2: 0.587 / CC star: 0.86 / % possible all: 99.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6y2e Resolution: 2.13→46.061 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.185 / SU B: 11.479 / SU ML: 0.255 / Average fsc free: 0.7286 / Average fsc work: 0.7357 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.21 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: 52.502 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→46.061 Å
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Refine LS restraints |
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LS refinement shell |
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