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Yorodumi- PDB-7zv7: Crystal structure of SARS Cov-2 main protease in complex with an ... -
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-Basic information
Entry | Database: PDB / ID: 7zv7 | ||||||
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Title | Crystal structure of SARS Cov-2 main protease in complex with an inhibitor 57 | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / SARS Cov-2 / 3CL / main protease | ||||||
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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' DNA helicase activity / 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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / 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 / 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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / copper ion binding / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / 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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.336 Å | ||||||
Authors | Rahimova, R. / Di Micco, S. / Marquez, J.A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2. Authors: Di Micco, S. / Rahimova, R. / Sala, M. / Scala, M.C. / Vivenzio, G. / Musella, S. / Andrei, G. / Remans, K. / Mammri, L. / Snoeck, R. / Bifulco, G. / Di Matteo, F. / Vestuto, V. / Campiglia, ...Authors: Di Micco, S. / Rahimova, R. / Sala, M. / Scala, M.C. / Vivenzio, G. / Musella, S. / Andrei, G. / Remans, K. / Mammri, L. / Snoeck, R. / Bifulco, G. / Di Matteo, F. / Vestuto, V. / Campiglia, P. / Marquez, J.A. / Fasano, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zv7.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zv7.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 7zv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zv7_validation.pdf.gz | 659.6 KB | Display | wwPDB validaton report |
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Full document | 7zv7_full_validation.pdf.gz | 660.9 KB | Display | |
Data in XML | 7zv7_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7zv7_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/7zv7 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zv7 | HTTPS FTP |
-Related structure data
Related structure data | 7zv5C 7zv8C 5rgsS 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: 33825.547 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: Protein/peptide | Type: Peptide-like / Class: Enzyme inhibitor / Mass: 444.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002411 |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.05 M Ammonium sulfate, 0.1 M Sodium Citrate, 15 % (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 |
Reflection | Resolution: 1.336→45.08 Å / Num. obs: 57524 / % possible obs: 94.2 % / Redundancy: 3 % / Biso Wilson estimate: 17.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.034 / Rrim(I) all: 0.019 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.336→1.359 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2972 / CC1/2: 0.804 / Rpim(I) all: 0.328 / Rrim(I) all: 0.572 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5rgs Resolution: 1.336→45.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.063 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso max: 126.35 Å2 / Biso mean: 20.94 Å2 / Biso min: 9.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.336→45.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.34→1.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 12.3077 Å / Origin y: 1.1608 Å / Origin z: 5.1211 Å
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Refinement TLS group | Selection details: { A|* } |