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Yorodumi- PDB-7jt0: Crystal structure of SARS-CoV-2 3CL protease in complex with MAC5576 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jt0 | ||||||
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Title | Crystal structure of SARS-CoV-2 3CL protease in complex with MAC5576 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / SARS-CoV-2 3CL protease / 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 / 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 / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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: 1.73 Å | ||||||
Authors | Iketani, S. / Forouhar, F. / Liu, H. / Hong, S.J. / Lin, F.-Y. / Nair, M.S. / Zask, A. / Huang, Y. / Xing, L. / Stockwell, B.R. ...Iketani, S. / Forouhar, F. / Liu, H. / Hong, S.J. / Lin, F.-Y. / Nair, M.S. / Zask, A. / Huang, Y. / Xing, L. / Stockwell, B.R. / Chavez, A. / Ho, D.D. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Authors: Iketani, S. / Forouhar, F. / Liu, H. / Hong, S.J. / Lin, F.Y. / Nair, M.S. / Zask, A. / Huang, Y. / Xing, L. / Stockwell, B.R. / Chavez, A. / Ho, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jt0.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jt0.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jt0_validation.pdf.gz | 775.9 KB | Display | wwPDB validaton report |
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Full document | 7jt0_full_validation.pdf.gz | 776.8 KB | Display | |
Data in XML | 7jt0_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 7jt0_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jt0 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jt0 | HTTPS FTP |
-Related structure data
Related structure data | 7jstSC 7jsuC 7jt7C 7jw8C S: Starting model for refinement C: citing same article (ref.) |
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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: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-LW1 / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Nonpolymer details | MAC5576 is a slowly hydrolyzed, unnatural substrate of 3CL, as confirmed by biochemical studies |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6 Details: 0.1 M sodium phosphate-monobasic, 0.1 M MES (pH 6), and 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→60.6 Å / Num. obs: 38900 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.73→1.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.69 / Num. unique obs: 3899 / CC1/2: 0.9 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JST Resolution: 1.73→47.03 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.67 / Stereochemistry target values: ML
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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 max: 150.59 Å2 / Biso mean: 42.403 Å2 / Biso min: 17.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→47.03 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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Refinement TLS params. | Method: refined / Origin x: -26.4727 Å / Origin y: 12.6631 Å / Origin z: 59.5781 Å
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Refinement TLS group |
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