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Yorodumi- PDB-7wqi: Crystal structure of SARS coronavirus main protease in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 7wqi | ||||||
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Title | Crystal structure of SARS coronavirus main protease in complex with PF07304814 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
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: 1.93 Å | ||||||
Authors | Lin, C. / Zhong, F.L. / Zhou, X.L. / Zeng, P. / Zhang, J. / Li, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of SARS coronavirus main protease in complex with PF07304814 Authors: Lin, C. / Zhong, F.L. / Zhou, X.L. / Zeng, P. / 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 | 7wqi.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wqi.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 7wqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wqi_validation.pdf.gz | 594 KB | Display | wwPDB validaton report |
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Full document | 7wqi_full_validation.pdf.gz | 605.3 KB | Display | |
Data in XML | 7wqi_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 7wqi_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/7wqi ftp://data.pdbj.org/pub/pdb/validation_reports/wq/7wqi | HTTPS FTP |
-Related structure data
Related structure data | 7dqzS 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
#1: Protein | Mass: 33169.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome-related coronavirus Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0C6U8, SARS coronavirus main proteinase #2: Chemical | #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: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting 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: BL02U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→57.18 Å / Num. obs: 210621 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.1041844493 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.93→2.03 Å / Rmerge(I) obs: 0.433 / Num. unique obs: 29523 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DQZ Resolution: 1.93→28.9681 Å / SU ML: 0.236891085947 / Cross valid method: NONE / σ(F): 1.95908010265 / Phase error: 28.7322180239 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: 48.1465084625 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→28.9681 Å
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Refine LS restraints |
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LS refinement shell |
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