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Yorodumi- PDB-8bs1: Room-temperature structure of SARS-CoV-2 Main protease at atmosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bs1 | ||||||
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Title | Room-temperature structure of SARS-CoV-2 Main protease at atmospheric pressure | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature / SARS-CoV-2 / Mpro / COVID-19 / PEPTIDE BINDING PROTEIN / virus protease | ||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / Resolution: 2.05 Å | ||||||
Authors | Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Rahmani Mashhour, A. / Meents, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: High-pressure macromolecular crystallography to explore the conformational space of proteins Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Assmann, M. / Zaun, H. / Kuballa, J. / Chapman, H.N. / Meents, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bs1.cif.gz | 225.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bs1.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bs1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/8bs1 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/8bs1 | HTTPS FTP |
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-Related structure data
Related structure data | 8bryC 8brzC 8bs0C 8bs2C 7ar5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 33841.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl was equilibrated against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ...Details: 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl was equilibrated against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Pressure: 101.325 kPa |
-Data collection
Diffraction | Ambient environment: air / Ambient pressure: 101.325 kPa / Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Apr 21, 2021 |
Diffraction measurement | Specimen support: kapton loop |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.477 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→26.18 Å / Num. obs: 17033 / % possible obs: 99.89 % / Redundancy: 15.2 % / Biso Wilson estimate: 42.93 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.2655 / Rpim(I) all: 0.06868 / Rrim(I) all: 0.2743 / Net I/σ(I): 6.73 |
Reflection shell | Resolution: 2.05→2.123 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.182 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1685 / CC1/2: 0.486 / CC star: 0.809 / Rpim(I) all: 0.6218 / Rrim(I) all: 2.27 / % possible all: 99.94 |
Cell measurement | Pressure: 101.325 kPa |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AR5 Resolution: 2.05→26.18 Å / SU ML: 0.2757 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1534 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 62.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→26.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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