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Yorodumi- PDB-2v6n: Crystal structures of the SARS-coronavirus main proteinase inacti... -
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-Basic information
Entry | Database: PDB / ID: 2v6n | ||||||
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Title | Crystal structures of the SARS-coronavirus main proteinase inactivated by benzotriazole compounds | ||||||
Components | REPLICASE POLYPROTEIN 1AB | ||||||
Keywords | VIRAL PROTEIN / THIOL PROTEASE / RNA REPLICATION / MAIN PROTEINASE / RIBOSOMAL FRAMESHIFT / SARS / PROTEASE / HYDROLASE / POLYPROTEIN | ||||||
Function / homology | Function and homology information cysteine-type deubiquitinase activity => GO:0004843 / : / : / cytoplasmic viral factory / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / suppression by virus of host type I interferon production / positive stranded viral RNA replication ...cysteine-type deubiquitinase activity => GO:0004843 / : / : / cytoplasmic viral factory / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / suppression by virus of host type I interferon production / positive stranded viral RNA replication / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K48-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / host cell membrane / 7-methylguanosine mRNA capping / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / helicase activity / membrane => GO:0016020 / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / methylation / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / single-stranded RNA binding / protein dimerization activity / 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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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: 1.98 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 | 2v6n.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v6n.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v6n_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 2v6n_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 2v6n_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2v6n_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/2v6n ftp://data.pdbj.org/pub/pdb/validation_reports/v6/2v6n | HTTPS FTP |
-Related structure data
Related structure data | 2vj1C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 / Fragment: SARS-COV MAIN PROTEINASE, RESIDUES 3241-3546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6WGN0, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-XP1 / |
#3: Chemical | ChemComp-MES / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has protein modification | Y |
Nonpolymer details | UPON BINDING TO THE MAIN PROTEINASE, THE NUCLEOPHILE CYS145 ATTACKS THE INHIBITOR 1-(4- ...UPON BINDING TO THE MAIN PROTEINASE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 6-8% PEG6000, 0.1 M MES PH 6.0, 3% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 26, 2006 / Details: BENT MIRROR |
Radiation | Monochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→65 Å / Num. obs: 30270 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 27.95 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UJ1 CHAIN A Resolution: 1.98→64.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.248 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.134 / 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: 33.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→64.55 Å
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Refine LS restraints |
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