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Yorodumi- PDB-6xmk: 1.70 A resolution structure of SARS-CoV-2 3CL protease in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xmk | ||||||
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Title | 1.70 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 7j | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROTEASE / severe acute respiratory syndrome coronavirus 2 / SARS-CoV-2 3CL protease Inhhibitors / COVID-19 / VIRAL PROTEIN / HYDROLASE-HYDROLASE 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 / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' DNA helicase activity / 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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / copper ion binding / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / 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 / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rathnayake, A.D. / Zheng, J. / Kim, Y. / Nguyen, H.N. / Chang, K.O. / Groutas, W.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Transl Med / Year: 2020 Title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Authors: Rathnayake, A.D. / Zheng, J. / Kim, Y. / Perera, K.D. / Mackin, S. / Meyerholz, D.K. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Groutas, W.C. / Chang, K.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xmk.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xmk.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xmk_validation.pdf.gz | 996.7 KB | Display | wwPDB validaton report |
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Full document | 6xmk_full_validation.pdf.gz | 1001.1 KB | Display | |
Data in XML | 6xmk_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 6xmk_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xmk ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xmk | HTTPS FTP |
-Related structure data
Related structure data | 6vgyC 6vgzC 6vh0C 6vh1C 6vh2C 6vh3C 6w2aC 6lu7S 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: 34068.805 Da / Num. of mol.: 2 / Fragment: Full Length Source method: isolated from a genetically manipulated source Details: N-terminal SUMO fusion with a TEV protease site Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pET His6 Sumo TEV LIC cloning vector (2S-T) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | ChemComp-PG4 / | #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: 2.24 Å3/Da / Density % sol: 45.17 % / Description: prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 20% (w/v) PEG 6000, 100 mM Tris, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 27, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.7→48.69 Å / Num. obs: 64757 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.6 / Num. measured all: 230552 / Scaling rejects: 179 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 1.7→28.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 25.05 / 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: 77.18 Å2 / Biso mean: 32.6087 Å2 / Biso min: 15.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→28.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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