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Yorodumi- PDB-7jkv: Crystal Structure of SARS-CoV-2 main protease in complex with an ... -
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-Basic information
Entry | Database: PDB / ID: 7jkv | ||||||
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Title | Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420 | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / 3C-like proteinase / VIRAL PROTEIN / SARS-CoV-2 / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / TRAF3-dependent IRF activation pathway / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Bulut, H. / Hattori, S.I. / Das, D. / Murayama, K. / Mitsuya, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication. Authors: Hattori, S.I. / Higashi-Kuwata, N. / Hayashi, H. / Allu, S.R. / Raghavaiah, J. / Bulut, H. / Das, D. / Anson, B.J. / Lendy, E.K. / Takamatsu, Y. / Takamune, N. / Kishimoto, N. / Murayama, K. ...Authors: Hattori, S.I. / Higashi-Kuwata, N. / Hayashi, H. / Allu, S.R. / Raghavaiah, J. / Bulut, H. / Das, D. / Anson, B.J. / Lendy, E.K. / Takamatsu, Y. / Takamune, N. / Kishimoto, N. / Murayama, K. / Hasegawa, K. / Li, M. / Davis, D.A. / Kodama, E.N. / Yarchoan, R. / Wlodawer, A. / Misumi, S. / Mesecar, A.D. / Ghosh, A.K. / Mitsuya, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jkv.cif.gz | 274.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jkv.ent.gz | 220.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jkv ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jkv | HTTPS FTP |
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-Related structure data
Related structure data | 6lu7S S: Starting model for refinement |
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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: 33882.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | ChemComp-1PE / | #4: 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: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 5.8, 15% polyethylene glycol (PEG) 6000, 3% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→56.14 Å / Num. obs: 158113 / % possible obs: 95.08 % / Redundancy: 2.68 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.05873 / Rrim(I) all: 0.0636 / Net I/σ(I): 10.52 |
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 1.05 / Num. unique obs: 10823 / Rsym value: 1.249 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 1.25→56.06 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.741 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.39 Å2 / Biso mean: 26.307 Å2 / Biso min: 10.18 Å2
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Refinement step | Cycle: final / Resolution: 1.25→56.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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