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Yorodumi- PDB-7eo7: Crystal structure of HCoV-NL63 3C-like protease in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eo7 | ||||||
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Title | Crystal structure of HCoV-NL63 3C-like protease in complex with an inhibitor Shikonin | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / HCoV | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm ...host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human coronavirus NL63 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24916621935 Å | ||||||
Authors | Gao, H.X. / Zhang, Y.T. / Zhou, X.L. / Zhong, F.L. / 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 | 7eo7.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eo7.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 7eo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eo7_validation.pdf.gz | 742.1 KB | Display | wwPDB validaton report |
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Full document | 7eo7_full_validation.pdf.gz | 747.5 KB | Display | |
Data in XML | 7eo7_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 7eo7_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/7eo7 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/7eo7 | HTTPS FTP |
-Related structure data
Related structure data | 7dqzC 7eo8C 7e6lS 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: 32763.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P0C6U6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-FNO / | #3: 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: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 3350, pH5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.24916621935→51.6408506815 Å / Num. obs: 29768 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.2342051286 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.25→2.31 Å / Rmerge(I) obs: 0.182 / Num. unique obs: 2086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7E6L Resolution: 2.24916621935→51.6408506815 Å / SU ML: 0.244127943788 / Cross valid method: FREE R-VALUE / σ(F): 1.45034303898 / Phase error: 22.585818759 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: 42.0004243652 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24916621935→51.6408506815 Å
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Refine LS restraints |
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LS refinement shell |
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