[English] 日本語
Yorodumi- PDB-2alv: X-ray structural analysis of SARS coronavirus 3CL proteinase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2alv | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structural analysis of SARS coronavirus 3CL proteinase in complex with designed anti-viral inhibitors | ||||||
Components | Replicase polyprotein 1ab | ||||||
Keywords | HYDROLASE / SARS / coronavirus / 3C / 3Cl / 3CLpro / proteinase / protease / inhibitor / anti-viral | ||||||
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 / endoribonuclease 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 / SARS-CoV-1 modulates host translation machinery / viral transcription / 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 / 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 / symbiont-mediated suppression of host gene expression / 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 / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 / viral protein processing / protein dimerization activity / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / 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 | SARS coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ghosh, A.K. / Xi, K. / Ratia, K. / Santarsiero, B.D. / Fu, W. / Harcourt, B.H. / Rota, P.A. / Baker, S.C. / Johnson, M.E. / Mesecar, A.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Design and synthesis of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease inhibitors. Authors: Ghosh, A.K. / Xi, K. / Ratia, K. / Santarsiero, B.D. / Fu, W. / Harcourt, B.H. / Rota, P.A. / Baker, S.C. / Johnson, M.E. / Mesecar, A.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2alv.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2alv.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 2alv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2alv_validation.pdf.gz | 743.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2alv_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | 2alv_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2alv_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/2alv ftp://data.pdbj.org/pub/pdb/validation_reports/al/2alv | HTTPS FTP |
-Related structure data
Related structure data | 1q2wS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33797.621 Da / Num. of mol.: 1 / Fragment: 3CL proteinase, residues 3242-3543 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Plasmid: PET11a / 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); Cysteine endopeptidases |
---|---|
#2: Chemical | ChemComp-CY6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 6.5 Details: PEG 20000, MPD, cacodylate, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→100 Å / Num. obs: 35975 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 / Χ2: 1.474 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 1.89→1.96 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.3 / Χ2: 1.47 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q2W Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 Stereochemistry target values: MAXIMUM LIKEHOOD TARGET FUNCTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 57.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.92 Å / Rfactor Rfree: 0.3867 / Rfactor Rwork: 0.3846 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|