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Yorodumi- PDB-7zb7: Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant Y54F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zb7 | ||||||
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Title | Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant Y54F at 1.63 A resolution | ||||||
Components | 3C-like proteinase nsp5 | ||||||
Keywords | HYDROLASE / SARS-COV-2 / MPRO | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Paknia, E. / Rabe von Pappenheim, F. / Funk, L.-M. / Tittmann, K. / Chari, A. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Authors: Funk, L.M. / Poschmann, G. / Rabe von Pappenheim, F. / Chari, A. / Stegmann, K.M. / Dickmanns, A. / Wensien, M. / Eulig, N. / Paknia, E. / Heyne, G. / Penka, E. / Pearson, A.R. / Berndt, C. ...Authors: Funk, L.M. / Poschmann, G. / Rabe von Pappenheim, F. / Chari, A. / Stegmann, K.M. / Dickmanns, A. / Wensien, M. / Eulig, N. / Paknia, E. / Heyne, G. / Penka, E. / Pearson, A.R. / Berndt, C. / Fritz, T. / Bazzi, S. / Uranga, J. / Mata, R.A. / Dobbelstein, M. / Hilgenfeld, R. / Curth, U. / Tittmann, K. #1: Journal: Biorxiv / Year: 2022 Title: Redox regulation of the SARS-CoV-2 main protease provides new opportunities for drug design Authors: Funk, L.M. / Poschmann, G. / Chari, A. / von Pappenheim, F.R. / Stegmann, K.M. / Dickmanns, A. / Eulig, N. / Wensien, M. / Paknia, E. / Heyne, G. / Penka, E. / Pearson, A.R. / Berndt, C. / ...Authors: Funk, L.M. / Poschmann, G. / Chari, A. / von Pappenheim, F.R. / Stegmann, K.M. / Dickmanns, A. / Eulig, N. / Wensien, M. / Paknia, E. / Heyne, G. / Penka, E. / Pearson, A.R. / Berndt, C. / Fritz, T. / Bazzi, S. / Uranga, J. / Mata, R.A. / Dobbelstein, M. / Hilgenfeld, R. / Curth, U. / Tittmann, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zb7.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zb7.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 7zb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zb7_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 7zb7_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 7zb7_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 7zb7_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/7zb7 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zb7 | HTTPS FTP |
-Related structure data
Related structure data | 7zb6C 7zb8C 6lu7S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 33809.547 Da / Num. of mol.: 1 / Mutation: Y54F 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 | ChemComp-DMS / #3: Chemical | ChemComp-GOL / | #4: 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: 1.96 Å3/Da / Density % sol: 37.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, DMSO, Sodium citrate, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→55.63 Å / Num. obs: 23935 / % possible obs: 92.2 % / Redundancy: 16.8 % / Biso Wilson estimate: 20.22 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.63→1.76 Å / Redundancy: 16.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1158 / CC1/2: 0.525 / Rpim(I) all: 0.665 / % possible all: 51.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LU7 Resolution: 1.63→55.63 Å / SU ML: 0.158 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.865 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→55.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.307419117 Å / Origin y: 0.811457171926 Å / Origin z: 5.01719343856 Å
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Refinement TLS group | Selection details: all |