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Yorodumi- PDB-6lu7: The crystal structure of COVID-19 main protease in complex with a... -
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-Basic information
Entry | Database: PDB / ID: 6lu7 | |||||||||||||||
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Title | The crystal structure of COVID-19 main protease in complex with an inhibitor N3 | |||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / protease | |||||||||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / Replication of the SARS-CoV-2 genome / snRNP Assembly / 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / 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 synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | |||||||||||||||
Authors | Liu, X. / Zhang, B. / Jin, Z. / Yang, H. / Rao, Z. | |||||||||||||||
Citation | Journal: Nature / Year: 2020 Title: Structure of Mprofrom SARS-CoV-2 and discovery of its inhibitors. Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / ...Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / Liu, X. / Yang, X. / Bai, F. / Liu, H. / Liu, X. / Guddat, L.W. / Xu, W. / Xiao, G. / Qin, C. / Shi, Z. / Jiang, H. / Rao, Z. / Yang, H. #1: Journal: Biorxiv / Year: 2020 Title: Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / ...Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / Liu, X. / Yang, X. / Bai, F. / Liu, H. / Liu, X. / Guddat, L. / Xu, W. / Xiao, G. / Qin, C. / Shi, Z. / Jiang, H. / Rao, Z. / Yang, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lu7.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lu7.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lu7_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 6lu7_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 6lu7_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 6lu7_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lu7 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lu7 | HTTPS FTP |
-Related structure data
Related structure data | 7bqyC 2hobS 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: 33825.547 Da / Num. of mol.: 1 / Fragment: 3C-like proteinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE |
#3: 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: 2.65 Å3/Da / Density % sol: 53.53 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6 Details: 2% polyethylene glycol (PEG) 6000, 3% DMSO, 1mM DTT, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0718 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→42.29 Å / Num. obs: 19455 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.16→2.22 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.472 / Num. unique obs: 1431 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HOB Resolution: 2.16→27.81 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.66 / 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: 89.99 Å2 / Biso mean: 42.82 Å2 / Biso min: 16.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.16→27.81 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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