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- PDB-7nuk: Crystal structure of SARS CoV2 main protease in complex with EG00... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nuk | ||||||
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Title | Crystal structure of SARS CoV2 main protease in complex with EG009 (modelled using PanDDA event map) | ||||||
![]() | 3C-like proteinase | ||||||
![]() | VIRAL PROTEIN / Protease / Complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oerlemans, R. / Eris, D. / Wang, M. / Sharpe, M. / Domling, A. / Groves, M.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.9 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nt1C ![]() 7nt2C ![]() 7nt3C ![]() 7ntvC ![]() 6lu7S 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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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.) ![]() ![]() Gene: ORF1ab / Production host: ![]() ![]() References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-USH / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6439114 Å3/Da / Density % sol: 53.506916 % |
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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 EG009 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM EG009 by adding the stock to ...Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock EG009 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM EG009 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00036 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→46.29 Å / Num. obs: 37312 / % possible obs: 99.3 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.071 / Rrim(I) all: 0.264 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.19→2.26 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.587 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3185 / CC1/2: 0.699 / Rpim(I) all: 0.741 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6lu7 Resolution: 2.19→46.29 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.179 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.231 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: 38.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→46.29 Å
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Refine LS restraints |
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LS refinement shell |
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