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Yorodumi- PDB-7pzq: Oxidized form of SARS-CoV-2 Main Protease determined by XFEL radiation -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pzq | |||||||||||||||
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Title | Oxidized form of SARS-CoV-2 Main Protease determined by XFEL radiation | |||||||||||||||
Components | 3C-like proteinase nsp5 | |||||||||||||||
Keywords | VIRAL PROTEIN / 3C-like protease / Main-Protease / Viral replication / Polyprotein maturation | |||||||||||||||
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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / 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 / host cell Golgi apparatus / methyltransferase cap1 / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent 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 | Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||||||||
Authors | Schubert, R. / Reinke, P. / Galchenkova, M. / Oberthuer, D. / Murillo, G.E.P. / Kim, C. / Bean, R. / Turk, D. / Hinrichs, W. / Middendorf, P. ...Schubert, R. / Reinke, P. / Galchenkova, M. / Oberthuer, D. / Murillo, G.E.P. / Kim, C. / Bean, R. / Turk, D. / Hinrichs, W. / Middendorf, P. / Round, A. / Schmidt, C. / Mills, G. / Kirkwood, H. / Han, H. / Koliyadu, J. / Bielecki, J. / Gelisio, L. / Sikorski, M. / Kloos, M. / Vakilii, M. / Yefanov, O.N. / Vagovic, P. / de-Wijn, R. / Letrun, R. / Guenther, S. / White, T.A. / Sato, T. / Srinivasan, V. / Kim, Y. / Chretien, A. / Han, S. / Brognaro, H. / Maracke, J. / Knoska, J. / Seychell, B.C. / Brings, L. / Norton-Baker, B. / Geng, T. / Dore, A.S. / Uetrecht, C. / Redecke, L. / Beck, T. / Lorenzen, K. / Betzel, C. / Mancuso, A.P. / Bajt, S. / Chapman, H.N. / Meents, A. / Lane, T.J. | |||||||||||||||
Funding support | Germany, European Union, 4items
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Citation | Journal: Nat Commun / Year: 2024 Title: SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds. Authors: Reinke, P.Y.A. / Schubert, R. / Oberthur, D. / Galchenkova, M. / Rahmani Mashhour, A. / Gunther, S. / Chretien, A. / Round, A. / Seychell, B.C. / Norton-Baker, B. / Kim, C. / Schmidt, C. / ...Authors: Reinke, P.Y.A. / Schubert, R. / Oberthur, D. / Galchenkova, M. / Rahmani Mashhour, A. / Gunther, S. / Chretien, A. / Round, A. / Seychell, B.C. / Norton-Baker, B. / Kim, C. / Schmidt, C. / Koua, F.H.M. / Tolstikova, A. / Ewert, W. / Pena Murillo, G.E. / Mills, G. / Kirkwood, H. / Brognaro, H. / Han, H. / Koliyadu, J. / Schulz, J. / Bielecki, J. / Lieske, J. / Maracke, J. / Knoska, J. / Lorenzen, K. / Brings, L. / Sikorski, M. / Kloos, M. / Vakili, M. / Vagovic, P. / Middendorf, P. / de Wijn, R. / Bean, R. / Letrun, R. / Han, S. / Falke, S. / Geng, T. / Sato, T. / Srinivasan, V. / Kim, Y. / Yefanov, O.M. / Gelisio, L. / Beck, T. / Dore, A.S. / Mancuso, A.P. / Betzel, C. / Bajt, S. / Redecke, L. / Chapman, H.N. / Meents, A. / Turk, D. / Hinrichs, W. / Lane, T.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pzq.cif.gz | 238.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pzq.ent.gz | 194.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pzq_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 7pzq_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 7pzq_validation.xml.gz | 26 KB | Display | |
Data in CIF | 7pzq_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/7pzq ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pzq | HTTPS FTP |
-Related structure data
Related structure data | 7pxzC 7z2kC 7akuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.22003/XFEL.EU-DATA-002696-00 / Details: XFEL raw image 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 Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7.5 Details: Vapor diffusion was set up with 2 uL MPro (35 mg/mL) and 2 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO. Seedstock was prepared by 100 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 4 uL seeds ...Details: Vapor diffusion was set up with 2 uL MPro (35 mg/mL) and 2 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO. Seedstock was prepared by 100 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 4 uL seeds from plate, vortex 5 times for 5 seconds, add 12.5 uL of MPro (35 mg/mL) and incubate at 18 deg overnight. Final sample was prepared in batch mode by adding 900 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 100 uL seedstock and 100 uL MPro (35 mg per mL). Add seedbeads (250 uL volume in 1.5 mL Eppi) and incubate overnight at 900 rpm and 18 deg. Crystals were soaked with crystallization buffer containing containing 4 mM Calpeptin. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3 Å |
Detector | Type: AGIPD / Detector: PIXEL / Date: Apr 16, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.63 Å / Num. obs: 38870 / % possible obs: 99.99 % / Redundancy: 355.55 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.9785 / CC star: 0.9945 / R split: 0.1693 / Net I/σ(I): 7.41 |
Reflection shell | Resolution: 2.218→2.257 Å / Redundancy: 20.3 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 1858 / CC1/2: 0.29 / CC star: 0.671 / R split: 1.213 / % possible all: 99.89 |
Serial crystallography sample delivery | Description: GDVN / Method: injection |
Serial crystallography sample delivery injection | Description: GDVN |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AKU Resolution: 2.25→24.61 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.25→24.61 Å
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