+Open data
-Basic information
Entry | Database: PDB / ID: 5b6o | |||||||||
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Title | Crystal structure of MS8104 | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | HYDROLASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
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 | Human SARS coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å | |||||||||
Authors | Wang, H. / Kim, Y. / Muramatsu, T. / Takemoto, C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity Authors: Muramatsu, T. / Takemoto, C. / Kim, Y.T. / Wang, H. / Nishii, W. / Terada, T. / Shirouzu, M. / Yokoyama, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b6o.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b6o.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 5b6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b6o ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b6o | HTTPS FTP |
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-Related structure data
Related structure data | 2ducSC 1uj1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34935.953 Da / Num. of mol.: 2 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Production host: CELL-FREE SYNTHESIS (others) References: UniProt: P0C6X7, SARS coronavirus main proteinase #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: 2.27 Å3/Da / Density % sol: 45.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: Sodium Chloride, PEG 4000 , pH 7.3, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2006 |
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. obs: 32224 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.846 % / Rsym value: 0.075 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.403 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DUC, 1UJ1 Resolution: 2.202→30.617 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 29.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.202→30.617 Å
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Refine LS restraints |
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LS refinement shell |
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