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Yorodumi- PDB-4ovz: X-Ray Structural and Biological Evaluation of a Series of Potent ... -
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-Basic information
Entry | Database: PDB / ID: 4ovz | ||||||
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Title | X-Ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-Like Proteases | ||||||
Components | (Papain-like proteinase) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / CoV / coronavirus / HCoV / human coronavirus / SARS / severe acute respiratory syndrome / MERS / Middle East respiratory syndrome / PLpro / protease inhibitor / complex / DUB / deubiquitinating enzyme / HYDROLASE-HYDROLASE 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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / 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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / 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 / 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 / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Baez-Santos, Y.M. / Mesecar, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases. Authors: Baez-Santos, Y.M. / Barraza, S.J. / Wilson, M.W. / Agius, M.P. / Mielech, A.M. / Davis, N.M. / Baker, S.C. / Larsen, S.D. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ovz.cif.gz | 223.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ovz.ent.gz | 179.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ovz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ovz_validation.pdf.gz | 981.6 KB | Display | wwPDB validaton report |
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Full document | 4ovz_full_validation.pdf.gz | 1002.1 KB | Display | |
Data in XML | 4ovz_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 4ovz_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/4ovz ftp://data.pdbj.org/pub/pdb/validation_reports/ov/4ovz | HTTPS FTP |
-Related structure data
Related structure data | 4ow0C 3mj5S 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 35584.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Strain: URBANI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase |
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#2: Protein | Mass: 35568.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Strain: URBANI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase |
-Non-polymers , 5 types, 85 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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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: 3.03 Å3/Da / Density % sol: 59.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM sodium citrate, pH 5.5, 40% (v/v) PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 24909 / Num. obs: 24909 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.3 |
Reflection shell | % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MJ5 Resolution: 2.5→35.746 Å / FOM work R set: 0.8156 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.57 / 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: 200.1 Å2 / Biso mean: 36.65 Å2 / Biso min: 8.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→35.746 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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