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Yorodumi- PDB-7lfv: Crystal structure of the SARS CoV-1 Papain-like protease in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lfv | ||||||||||||
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Title | Crystal structure of the SARS CoV-1 Papain-like protease in complex with peptide inhibitor VIR251 | ||||||||||||
Components |
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Keywords | Hydrolase/Hydrolas Inhibitor / COVID-19 / CORONAVIRUS / SARS / COV-1 / COV-2 / PAPAIN-LIKE PROTEASE / PLPRO / DEUBIQUITINATING ENZYME / UBIQUITIN / ACTIVITY-BASED PROBE / Hydrolase-Hydrolas Inhibitor complex | ||||||||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / methylation / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å | ||||||||||||
Authors | Olsen, S.K. / Lv, Z. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell Rep / Year: 2021 Title: A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Authors: Patchett, S. / Lv, Z. / Rut, W. / Bekes, M. / Drag, M. / Olsen, S.K. / Huang, T.T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lfv.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lfv.ent.gz | 218.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lfv ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lfv | HTTPS FTP |
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-Related structure data
Related structure data | 7lfuC 6wuuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules BADF
#1: Protein | Mass: 36688.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus Gene: 1a / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) RIL CODON PLUS References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase #2: Protein/peptide | |
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-Non-polymers , 6 types, 149 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-NH4 / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | Peptide covalently linked to active site Cys |
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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: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 16% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 108 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→132.68 Å / Num. obs: 42208 / % possible obs: 99.9 % / Redundancy: 38.7 % / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 30.9 / Num. measured all: 1632487 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WUU Resolution: 2.23→53.34 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
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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 max: 199.04 Å2 / Biso mean: 65.5255 Å2 / Biso min: 31.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→53.34 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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