[English] 日本語
Yorodumi- PDB-1uk4: Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uk4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / anti-parallel b-barrel / anti-parallel a-helices / an inhibitor | |||||||||
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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription ...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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription / 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 / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | SARS coronavirus synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uk4.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uk4.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1uk4 ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1uk4 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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 / Gene: rep / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) References: UniProt: P0C6X7, SARS coronavirus main proteinase #2: Protein/peptide | Mass: 594.059 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: the sequence occurs peptide synthesis / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.34 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.5→50 Å / Num. all: 18499 / Num. obs: 17623 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.48→2.54 Å / % possible all: 95.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 22614 / % possible obs: 98.4 % / Redundancy: 4.2 % / Num. measured all: 78378 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 96.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.216 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|