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Yorodumi- PDB-7tiv: Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB48 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tiv | ||||||||||||||||||||||||
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Title | Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB48 | ||||||||||||||||||||||||
Components | 3C-like proteinase nsp5 | ||||||||||||||||||||||||
Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN / VIRAL PROTEIN-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 / 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: 2.08 Å | ||||||||||||||||||||||||
Authors | Forouhar, F. / Liu, H. / Iketani, S. / Zack, A. / Khanizeman, N. / Bednarova, E. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. ...Forouhar, F. / Liu, H. / Iketani, S. / Zack, A. / Khanizeman, N. / Bednarova, E. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, S.J. / Quinn, C. / Li, W. / Shion, H. / Jurtschenko, C. / Lauber, M.A. / McDonald, T. / Stokes, M.E. / Hurst, B. / Rovis, T. / Chavez, A. / Ho, D.D. / Stockwell, B.R. | ||||||||||||||||||||||||
Funding support | 7items
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Citation | Journal: Nat Commun / Year: 2022 Title: Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Authors: Liu, H. / Iketani, S. / Zask, A. / Khanizeman, N. / Bednarova, E. / Forouhar, F. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, ...Authors: Liu, H. / Iketani, S. / Zask, A. / Khanizeman, N. / Bednarova, E. / Forouhar, F. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, S.J. / Quinn, C. / Li, W. / Shion, H. / Xia, X. / Daniels, J.D. / Bartolo-Cruz, M. / Farina, M. / Rajbhandari, P. / Jurtschenko, C. / Lauber, M.A. / McDonald, T. / Stokes, M.E. / Hurst, B.L. / Rovis, T. / Chavez, A. / Ho, D.D. / Stockwell, B.R. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tiv.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tiv.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tiv_validation.pdf.gz | 787.3 KB | Display | wwPDB validaton report |
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Full document | 7tiv_full_validation.pdf.gz | 790.3 KB | Display | |
Data in XML | 7tiv_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7tiv_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/7tiv ftp://data.pdbj.org/pub/pdb/validation_reports/ti/7tiv | HTTPS FTP |
-Related structure data
Related structure data | 7tiaC 7tiuC 7tiwC 7tixC 7tiyC 7tizC 7tj0C 7jsuS S: Starting model for refinement 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 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 Production host: Escherichia coli (E. coli) References: UniProt: P0DTC1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-W48 / ( |
#3: Chemical | ChemComp-MG / |
#4: 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: 2.84 Å3/Da / Density % sol: 56.66 % / Description: block-shaped |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 5 Details: 0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (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: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 8, 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: 1.88→59.23 Å / Num. obs: 30383 / % possible obs: 98.5 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.256 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.88→1.92 Å / Rmerge(I) obs: 2.347 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1617 / CC1/2: 0.432 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JSU Resolution: 2.08→48.9 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.29 / 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: 124.66 Å2 / Biso mean: 48.2361 Å2 / Biso min: 20.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→48.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: -5.3473 Å / Origin y: -0.6977 Å / Origin z: 12.2962 Å
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Refinement TLS group |
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