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Yorodumi- PDB-1uk2: Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At... -
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-Basic information
Entry | Database: PDB / ID: 1uk2 | ||||||
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Title | Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) At pH8.0 | ||||||
Components | 3C-LIKE PROTEINASE | ||||||
Keywords | HYDROLASE / anti-parallel b-barrel / anti-parallel a-helices | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yang, H. / Yang, M. / Liu, Y. / Bartlam, M. / Ding, Y. / Lou, Z. / Sun, L. / Zhou, Z. / Ye, S. / Anand, K. ...Yang, H. / Yang, M. / Liu, Y. / Bartlam, M. / Ding, Y. / Lou, Z. / Sun, L. / Zhou, Z. / Ye, S. / Anand, K. / Pang, H. / Gao, G.F. / Hilgenfeld, R. / Rao, Z. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor Authors: Yang, H. / Yang, M. / Ding, Y. / Liu, Y. / Lou, Z. / Zhou, Z. / Sun, L. / Mo, L. / Ye, S. / Pang, H. / Gao, G.F. / Anand, K. / Bartlam, M. / Hilgenfeld, R. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uk2.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uk2.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uk2_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 1uk2_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 1uk2_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1uk2_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1uk2 ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1uk2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: 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: 2.4 Å3/Da / Density % sol: 48.27 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES, DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 31899 / Num. obs: 29475 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 100 |
Reflection | *PLUS Num. obs: 31275 / Redundancy: 4.4 % / Num. measured all: 119770 / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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