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Yorodumi- PDB-7mbi: Structure of SARS-CoV2 3CL protease covalently bound to peptidomi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mbi | |||||||||
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Title | Structure of SARS-CoV2 3CL protease covalently bound to peptidomimetic inhibitor | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / 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 / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 / symbiont-mediated suppression of host NF-kappaB cascade / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / 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: 2.15 Å | |||||||||
Authors | Khan, M.B. / Lu, J. / Young, H.S. / Lemieux, M.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Peptidomimetic alpha-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability. Authors: Bai, B. / Belovodskiy, A. / Hena, M. / Kandadai, A.S. / Joyce, M.A. / Saffran, H.A. / Shields, J.A. / Khan, M.B. / Arutyunova, E. / Lu, J. / Bajwa, S.K. / Hockman, D. / Fischer, C. / Lamer, ...Authors: Bai, B. / Belovodskiy, A. / Hena, M. / Kandadai, A.S. / Joyce, M.A. / Saffran, H.A. / Shields, J.A. / Khan, M.B. / Arutyunova, E. / Lu, J. / Bajwa, S.K. / Hockman, D. / Fischer, C. / Lamer, T. / Vuong, W. / van Belkum, M.J. / Gu, Z. / Lin, F. / Du, Y. / Xu, J. / Rahim, M. / Young, H.S. / Vederas, J.C. / Tyrrell, D.L. / Lemieux, M.J. / Nieman, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mbi.cif.gz | 555.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mbi.ent.gz | 382.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mbi_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7mbi_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7mbi_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 7mbi_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/7mbi ftp://data.pdbj.org/pub/pdb/validation_reports/mb/7mbi | HTTPS FTP |
-Related structure data
Related structure data | 6wtmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 4 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 O103:H2 (bacteria) / Strain (production host): 12009 References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | ChemComp-YWJ / #3: Chemical | ChemComp-FN7 / | #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2 M Sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane 8.5 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→37.14 Å / Num. obs: 132051 / % possible obs: 99.69 % / Redundancy: 13.12 % / Biso Wilson estimate: 49.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.73 |
Reflection shell | Resolution: 2.15→2.227 Å / Num. unique obs: 6772 / CC1/2: 0.767 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WTM Resolution: 2.15→37.14 Å / SU ML: 0.3654 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 33.5306 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: 62.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→37.14 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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