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Yorodumi- PDB-7eo8: Crystal structure of SARS coronavirus main protease in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 7eo8 | ||||||
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Title | Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / SARS coronavirus main protease 3CL | ||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 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 / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28085164536 Å | ||||||
Authors | Zhang, Y.T. / Gao, H.X. / Zhou, H. / Zhong, F.L. / Hu, X.H. / Zhou, X.L. / Lin, C. / Wang, Q.S. / Li, J. / Zhang, J. | ||||||
Funding support | 1items
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Citation | Journal: J.Virol. / Year: 2022 Title: Structure-Based Discovery and Structural Basis of a Novel Broad-Spectrum Natural Product against the Main Protease of Coronavirus. Authors: Zhang, Y. / Gao, H. / Hu, X. / Wang, Q. / Zhong, F. / Zhou, X. / Lin, C. / Yang, Y. / Wei, J. / Du, W. / Huang, H. / Zhou, H. / He, W. / Zhang, H. / Zhang, Y. / McCormick, P.J. / Fu, J. / ...Authors: Zhang, Y. / Gao, H. / Hu, X. / Wang, Q. / Zhong, F. / Zhou, X. / Lin, C. / Yang, Y. / Wei, J. / Du, W. / Huang, H. / Zhou, H. / He, W. / Zhang, H. / Zhang, Y. / McCormick, P.J. / Fu, J. / Wang, D. / Fu, Y. / Lu, X. / Zhang, T. / Duan, J. / Qin, B. / Jiang, H. / Luo, J. / Zhang, Y. / Chen, Q. / Luo, Q. / Cheng, L. / Zhang, Z. / Zhang, J. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eo8.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eo8.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 7eo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eo8_validation.pdf.gz | 697.4 KB | Display | wwPDB validaton report |
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Full document | 7eo8_full_validation.pdf.gz | 707.6 KB | Display | |
Data in XML | 7eo8_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 7eo8_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/7eo8 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/7eo8 | HTTPS FTP |
-Related structure data
Related structure data | 7dqzSC 7eo7C 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
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome-related coronavirus Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0C6U8, SARS coronavirus main proteinase #2: Chemical | ChemComp-FNO / | 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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→46.03 Å / Num. obs: 35348 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 44.1114493017 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.28→2.4 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 5295 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DQZ Resolution: 2.28085164536→27.3269337675 Å / SU ML: 0.310019876762 / Cross valid method: NONE / σ(F): 1.96354714251 / Phase error: 37.5282727065 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: 59.1759847793 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28085164536→27.3269337675 Å
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Refine LS restraints |
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LS refinement shell |
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