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Yorodumi- PDB-6w79: Structure of SARS-CoV main protease bound to potent broad-spectru... -
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-Basic information
Entry | Database: PDB / ID: 6w79 | ||||||
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Title | Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent inhibitor X77 | ||||||
Components | Main protease3C-like protease | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / main protease / Mpro / 3C-like / 3CLpro / non-covalent / inhibitor / SARS / SARS-CoV / COVID-19 / X77 / broad-spectrum / coronavirus / drug / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN / 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | SARS-COV-2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Mesecar, A.D. / StJohn, S. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19) Authors: Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w79.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w79.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 6w79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w79 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w79 | HTTPS FTP |
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-Related structure data
Related structure data | 6w63C 6w81C 6wcoC 4mdsS 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: 33876.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS-COV-2 (virus) / Strain: COVID-19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C6X7*PLUS | ||||
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#2: Chemical | ChemComp-DMS / | ||||
#3: Chemical | ChemComp-X77 / | ||||
#4: Chemical | #5: 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 grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 3 uL drops that were formed by adding 1 uL of purified SARS-3CLpro (10 mg/mL) that had been incubated for three hours with a 3 molar excess of the of compound X77, and 2 uL of reservoir ...Details: 3 uL drops that were formed by adding 1 uL of purified SARS-3CLpro (10 mg/mL) that had been incubated for three hours with a 3 molar excess of the of compound X77, and 2 uL of reservoir solution: 3 mM DTT, 50 mM MES pH 6.0, 40 mM KCl, 1% MPD, and 5% PEG-10K Temp details: Cold room for crystals |
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-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Dry nitrogen stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→100 Å / Num. obs: 77810 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 18.31 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.049 / Χ2: 1.45 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3875 / CC1/2: 0.908 / CC star: 0.976 / Rpim(I) all: 0.286 / Rrim(I) all: 0.62 / Χ2: 0.893 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDS Resolution: 1.46→32.28 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.8421 / Details: TLS parameters were included into the refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→32.28 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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