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Yorodumi- PDB-7tvx: The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tvx | ||||||
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Title | The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with masitinib | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE/INHIBITOR / SARS-COV-2 / COVID-19 / 3CL / MAIN PROTEASE / MASITINIB / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 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 / 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 / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.094 Å | ||||||
Authors | Tan, K. / Maltseva, N.I. / Endres, M.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of SARS-CoV-2 Omicron Mpro (P132H) in complex with masitinib Authors: Tan, K. / Maltseva, N.I. / Endres, M.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tvx.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tvx.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tvx_validation.pdf.gz | 655.2 KB | Display | wwPDB validaton report |
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Full document | 7tvx_full_validation.pdf.gz | 660.2 KB | Display | |
Data in XML | 7tvx_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7tvx_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/7tvx ftp://data.pdbj.org/pub/pdb/validation_reports/tv/7tvx | HTTPS FTP |
-Related structure data
Related structure data | 7ju7S S: Starting model for refinement |
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Similar structure data |
-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 Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) References: UniProt: P0DTC1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-G65 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Ammonium Acetate, 0.1 M Bis-Tris: HCl, 10 % (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97936 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2022 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 2.094→43.53 Å / Num. obs: 20545 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 44.4704456037 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.062 / Rrim(I) all: 0.106 / Χ2: 1.567 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 980 / CC1/2: 0.518 / CC star: 0.826 / Rpim(I) all: 0.508 / Rrim(I) all: 0.83 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JU7 Resolution: 2.094→43.53 Å / SU ML: 0.2424663871 / Cross valid method: FREE R-VALUE / σ(F): 1.33794008837 / Phase error: 25.4798641749 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: 60.3928147422 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.094→43.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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