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Yorodumi- PDB-7ntv: Crystal structure of SARS CoV2 main protease in complex with DN_E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ntv | ||||||
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Title | Crystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map) | ||||||
Components | 3C-like proteinase | ||||||
Keywords | VIRAL PROTEIN / Protease / Complex | ||||||
Function / homology | Function and homology information viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.065 Å | ||||||
Authors | Oerlemans, R. / Eris, D. / Wang, M. / Sharpe, M. / Domling, A. / Groves, M.R. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Authors: Sutanto, F. / Shaabani, S. / Oerlemans, R. / Eris, D. / Patil, P. / Hadian, M. / Wang, M. / Sharpe, M.E. / Groves, M.R. / Domling, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ntv.cif.gz | 242.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ntv.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ntv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/7ntv ftp://data.pdbj.org/pub/pdb/validation_reports/nt/7ntv | HTTPS FTP |
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-Related structure data
Related structure data | 7nt1C 7nt2C 7nt3C 7nukC 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: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-US8 / | #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: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 by adding the stock to ...Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.065→49.423 Å / Num. obs: 44110 / % possible obs: 99.82 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.044 / Rrim(I) all: 0.164 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.065→2.119 Å / Redundancy: 13.75 % / Rmerge(I) obs: 1.961 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3361 / CC1/2: 0.71 / Rpim(I) all: 0.54 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6lu7 Resolution: 2.065→49.423 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.568 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.164 Details: Hydrogens have been added in their riding positions
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.474 Å2
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Refinement step | Cycle: LAST / Resolution: 2.065→49.423 Å
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Refine LS restraints |
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LS refinement shell |
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