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Yorodumi- PDB-2hob: Crystal structure of SARS-CoV main protease with authentic N and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hob | |||||||||
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Title | Crystal structure of SARS-CoV main protease with authentic N and C-termini in complex with a Michael acceptor N3 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV / main protease / michael acceptor N3 | |||||||||
Function / homology | Function and homology information viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / : / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / protein K48-linked deubiquitination / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / 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 / RNA-templated transcription / viral transcription / SARS-CoV-1 modulates host translation machinery / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / symbiont-mediated suppression of host gene expression / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / host cell cytoplasm / 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 / protein dimerization activity / 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 | SARS coronavirus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Xue, X. / Yang, H. / Shen, W. / Zhao, Q. / Li, J. / Rao, Z. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Production of authentic SARS-CoV M(pro) with enhanced activity: application as a novel tag-cleavage endopeptidase for protein overproduction Authors: Xue, X. / Yang, H. / Shen, W. / Zhao, Q. / Li, J. / Yang, K. / Chen, C. / Jin, Y. / Bartlam, M. / Rao, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hob.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hob.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hob_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 2hob_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 2hob_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 2hob_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/2hob ftp://data.pdbj.org/pub/pdb/validation_reports/ho/2hob | HTTPS FTP |
-Related structure data
Related structure data | 2h2zC 1uk3S 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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Details | The crystal belongs to space group C2, and each asymmetric unit contains only one protomer of a typical dimer. The two protomers in the dimer are related by the crystallographic 2-fold symmetry axis. |
-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 / Fragment: 3C-like proteinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2% polyethylene glycol(PEG) 6000, 3% DMSO, 1mM DTT, 0.1M [2-(N-morpholino)ethanesulfonic acid] (Mes) buffer (pH 6.0), with a protein concentration of 5mg/ml. Inhibitor N3 was dissolved in 7. ...Details: 2% polyethylene glycol(PEG) 6000, 3% DMSO, 1mM DTT, 0.1M [2-(N-morpholino)ethanesulfonic acid] (Mes) buffer (pH 6.0), with a protein concentration of 5mg/ml. Inhibitor N3 was dissolved in 7.5% PEG 6000, 6% DMSO, and 0.1M Mes (pH 6.0) with a concentration of 10mM (supersaturation). Then, a 3 micro-l aliquot of such solution was added to the drop, and the crystals were soaked for approximately 2-6 days., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2006 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 32068 / % possible obs: 99.6 % |
Reflection shell | Resolution: 1.95→2.02 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UK3 Resolution: 1.95→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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