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Yorodumi- PDB-2vj1: A Structural View of the Inactivation of the SARS-Coronavirus Mai... -
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-Basic information
Entry | Database: PDB / ID: 2vj1 | |||||||||
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Title | A Structural View of the Inactivation of the SARS-Coronavirus Main Proteinase by Benzotriazole Esters | |||||||||
Components | SARS CORONAVIRUS MAIN PROTEINASE | |||||||||
Keywords | HYDROLASE / SARS / PROTEASE / POLYPROTEIN / THIOL PROTEASE / RIBOSOMAL FRAMESHIFT / SARS CORONAVIRUS MAIN PROTEINASE | |||||||||
Function / homology | Function and homology information cysteine-type deubiquitinase activity => GO:0004843 / 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 / viral transcription ...cysteine-type deubiquitinase activity => GO:0004843 / 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 / viral transcription / SARS-CoV-1 modulates host translation machinery / host cell membrane / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / 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 / transferase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / membrane => GO:0016020 / 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 / RNA helicase / induction by virus of host autophagy / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | HUMAN SARS CORONAVIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Verschueren, K.H.G. / Pumpor, K. / Anemueller, S. / Mesters, J.R. / Hilgenfeld, R. | |||||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: A Structural View of the Inactivation of the Sars Coronavirus Main Proteinase by Benzotriazole Esters. Authors: Verschueren, K.H.G. / Pumpor, K. / Anemueller, S. / Chen, S. / Mesters, J.R. / Hilgenfeld, R. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vj1.cif.gz | 254.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vj1.ent.gz | 207.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vj1_validation.pdf.gz | 475.6 KB | Display | wwPDB validaton report |
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Full document | 2vj1_full_validation.pdf.gz | 489.5 KB | Display | |
Data in XML | 2vj1_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2vj1_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vj1 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vj1 | HTTPS FTP |
-Related structure data
Related structure data | 2v6nC 1uj1S 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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Unit cell |
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-Components
#1: Protein | Mass: 34343.129 Da / Num. of mol.: 2 / Fragment: RESIDUES 3242-3544 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: A7J8L3, UniProt: P0C6X7*PLUS, EC: 3.4.34.- #2: Chemical | #3: Chemical | ChemComp-BEZ / | #4: Chemical | ChemComp-XP1 / | #5: 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: 2.5 Å3/Da / Density % sol: 50.2 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 5% PEG10000, 0.1M MES PH6.5, 3% ETHYLNE GLYCOL, 50MM NH4-ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8157 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 7, 2005 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8157 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.27 Å / Num. obs: 31422 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.25→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.91 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UJ1 Resolution: 2.25→65.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.502 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→65.94 Å
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