+Open data
-Basic information
Entry | Database: PDB / ID: 8gzb | ||||||
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Title | SARS-CoV-2 3CLpro | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | VIRAL PROTEIN / Inhibitor / Complex / RECOMBINATION / HYDROLASE | ||||||
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 / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.7 Å | ||||||
Authors | Wang, F. / Cen, Y.X. / Tian, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2023 Title: Nature-inspired catalytic asymmetric rearrangement of cyclopropylcarbinyl cation. Authors: Li, Q.H. / Zhang, G.S. / Wang, F. / Cen, Y. / Liu, X.L. / Zhang, J.W. / Wang, Y.H. / Lee, A.W.M. / Gao, D. / Lin, G.Q. / Tian, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gzb.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gzb.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 8gzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/8gzb ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gzb | HTTPS FTP |
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-Related structure data
Related structure data | 7wo3S S: Starting model for refinement |
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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-EDO / |
#3: Chemical | ChemComp-KM6 / |
#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: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 25% PEG 3350, 0.2M ammonium sulfate, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9774 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.66 Å / Num. obs: 7404 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.878 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.7→2.83 Å / Rmerge(I) obs: 0.82 / Num. unique obs: 974 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WO3 Resolution: 2.7→43.49 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4035 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: 45.05 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.49 Å
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Refine LS restraints |
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LS refinement shell |
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