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Yorodumi- PDB-7k0g: 1.85 A resolution structure of SARS-CoV 3CL protease in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k0g | ||||||
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Title | 1.85 A resolution structure of SARS-CoV 3CL protease in complex with deuterated GC376 | ||||||
Components | Replicase polyprotein 1a | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / PROTEASE / severe acute respiratory syndrome coronavirus / SARS 3CL protease Inhhibitors / hydrolase / deuterated hydrolase inhibitor / Hydrolase-Hydrolase 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 | Human SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Chamandi, S.D. / Nguyen, H.N. / Kim, Y. / Chang, K.O. / Groutas, W.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection. Authors: Dampalla, C.S. / Zheng, J. / Perera, K.D. / Wong, L.R. / Meyerholz, D.K. / Nguyen, H.N. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Kim, Y. / Perlman, S. / Groutas, W.C. / Chang, K.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k0g.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k0g.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 7k0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k0g_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7k0g_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7k0g_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7k0g_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/7k0g ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k0g | HTTPS FTP |
-Related structure data
Related structure data | 7k0eC 7k0fC 7k0hC 6w2aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34460.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal hexahistidine tag / Source: (gene. exp.) Human SARS coronavirus / Gene: 1a / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-K36 / ( |
#3: Chemical | ChemComp-B1S / ( |
#4: Water | ChemComp-HOH / |
Compound details | Both B1S and K36 are deuterated in this structure |
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: 1.89 Å3/Da / Density % sol: 35.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% (w/v) PEG 3350, 0.2 M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.85→47.94 Å / Num. obs: 23106 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.7 / Num. measured all: 187771 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W2A Resolution: 1.85→34.64 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 26.07 / 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: 108.29 Å2 / Biso mean: 40.1913 Å2 / Biso min: 18.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→34.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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