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Yorodumi- PDB-7lcq: N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL... -
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-Basic information
Entry | Database: PDB / ID: 7lcq | |||||||||
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Title | N-terminal finger stabilizes feline drug GC376 in coronavirus 3CL protease | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / COVID-19 / SARS-CoV-1 / 3CLpro / coronavirus / main protease / kinetics / SARS / Hydrolase-Hydrolase Inhibitor complex / 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 transcription ...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 transcription / Transferases; Transferring one-carbon groups; Methyltransferases / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Khan, M.B. / Arutyunova, E. / Young, H.S. / Lemieux, M.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 M pro Dimer. Authors: Arutyunova, E. / Khan, M.B. / Fischer, C. / Lu, J. / Lamer, T. / Vuong, W. / van Belkum, M.J. / McKay, R.T. / Tyrrell, D.L. / Vederas, J.C. / Young, H.S. / Lemieux, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lcq.cif.gz | 223.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lcq.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lcq_validation.pdf.gz | 834.8 KB | Display | wwPDB validaton report |
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Full document | 7lcq_full_validation.pdf.gz | 843.8 KB | Display | |
Data in XML | 7lcq_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7lcq_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/7lcq ftp://data.pdbj.org/pub/pdb/validation_reports/lc/7lcq | HTTPS FTP |
-Related structure data
Related structure data | 7lcpC 2q6gS 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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus Gene: rep, 1a-1b / Production host: Escherichia coli O103:H2 (bacteria) / Strain (production host): 12009 References: UniProt: P0C6X7, SARS coronavirus main proteinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-UED / | #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: 3.42 Å3/Da / Density % sol: 64.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 Details: 7% PEG 8000, 1 mM MES pH 6.0, 1mM DTT, 3% ethylene glycol and 3% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→33.19 Å / Num. obs: 24292 / % possible obs: 96.94 % / Redundancy: 4.5 % / Biso Wilson estimate: 70 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.77 |
Reflection shell | Resolution: 2.15→33.19 Å / Num. unique obs: 2322 / CC1/2: 0.607 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2q6g Resolution: 2.15→33.19 Å / SU ML: 0.3868 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1488 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The data were collected and processed to 1.31 A, but the structure was refined using only data to 2.15 A
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→33.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.84378689482 Å / Origin y: -39.2227181691 Å / Origin z: 10.820504832 Å
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Refinement TLS group | Selection details: all |