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- PDB-7rn0: Crystal structure of the SARS-CoV-2 (COVID-19) main protease in c... -
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Basic information
Entry | Database: PDB / ID: 7rn0 | |||||||||
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Title | Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-57-3R | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Mpro / inhibitor / main protease / 3cl / SARS / SARS-CoV-2 / COVID / COVID-19 / VIRAL PROTEIN / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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, hydrolytic mechanism / 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 / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / copper ion binding / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / DNA clamp loader activity / symbiont-mediated suppression of host gene expression / RNA-directed 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sacco, M. / Chen, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity. Authors: Ma, C. / Xia, Z. / Sacco, M.D. / Hu, Y. / Townsend, J.A. / Meng, X. / Choza, J. / Tan, H. / Jang, J. / Gongora, M.V. / Zhang, X. / Zhang, F. / Xiang, Y. / Marty, M.T. / Chen, Y. / Wang, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.3 KB | Display | ![]() |
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Full document | ![]() | 813.3 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kx5SC ![]() 7rn1C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-5ZB / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25 % 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 11614 / % possible obs: 92.4 % / Redundancy: 2.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.05 / Rrim(I) all: 0.087 / Net I/σ(I): 7.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.8 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7KX5 Resolution: 2.25→48.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.394 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.668 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.6 Å2 / Biso mean: 53.388 Å2 / Biso min: 25.49 Å2
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Refinement step | Cycle: final / Resolution: 2.25→48.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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