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Yorodumi- PDB-2a5i: Crystal structures of SARS coronavirus main peptidase inhibited b... -
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-Basic information
Entry | Database: PDB / ID: 2a5i | ||||||
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Title | Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in the space group C2 | ||||||
Components | 3C-like peptidase | ||||||
Keywords | HYDROLASE / cysteine peptidase / 3C-like / N-finger / chymotrypsin-like fold / long loop / alpha-helical domain / dimer / catalytic dyad / specificity pockets / aza-peptide epoxide / substrate-like inhibitor / C-S covalent bond / epoxide stereochemistry | ||||||
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: 1.88 Å | ||||||
Authors | Lee, T.-W. / Cherney, M.M. / Huitema, C. / Liu, J. / James, K.E. / Powers, J.C. / Eltis, L.D. / James, M.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide Authors: Lee, T.-W. / Cherney, M.M. / Huitema, C. / Liu, J. / James, K.E. / Powers, J.C. / Eltis, L.D. / James, M.N. | ||||||
History |
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Remark 600 | HETEROGEN BEFORE BINDING TO THE PEPTIDASE, CBM, CBO AND OBN FORM AN EPOXIDE RING IN AZP. UPON ...HETEROGEN BEFORE BINDING TO THE PEPTIDASE, CBM, CBO AND OBN FORM AN EPOXIDE RING IN AZP. UPON BINDING TO THE PEPTIDASE, CYS145 SG NUCLEOPHILLICALLY ATTACKS CBM, RESULTING IN THE OPENING OF THE RING AND THE INVERSION OF THE CONFIGURATIONS OF CBM AND CBO. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5i.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5i.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a5i_validation.pdf.gz | 769.7 KB | Display | wwPDB validaton report |
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Full document | 2a5i_full_validation.pdf.gz | 781.8 KB | Display | |
Data in XML | 2a5i_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2a5i_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5i ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5i | HTTPS FTP |
-Related structure data
Related structure data | 2a5aSC 2a5kC 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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2 |
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Unit cell |
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Details | The protease is a homodimer. Each asymmetric unit contains only one protomer. The other protomer of the dimer is generated from the protomer in the asymmetric unit by the operation -x, y, -z. |
-Components
#1: Protein | Mass: 33876.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Plasmid: PT7HSP2 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-AZP / ( |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 3.35 Å3/Da / Density % sol: 63.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium acetate, PEG 10000, ethylene glycol, dimethyl sulfoxide, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 35576 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.88→1.95 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2A5A Resolution: 1.88→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.384 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The low reolution limit for data collection and processing was 50 A. For refinement, `less' low resolution data and the low resolution limit was set upwards to 40 A. But there is actually no ...Details: The low reolution limit for data collection and processing was 50 A. For refinement, `less' low resolution data and the low resolution limit was set upwards to 40 A. But there is actually no data in the resolution range 50 - 32.3 A.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.973 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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