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Yorodumi- PDB-3m3t: SARS-CoV main protease monomeric Arg298Ala mutant with N-terminal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m3t | ||||||
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Title | SARS-CoV main protease monomeric Arg298Ala mutant with N-terminal additional residues (Gly-Ser) | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE / sars protease Arg298Ala monomeric | ||||||
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 / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / methylation / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shi, J.H. / Song, J.X. | ||||||
Citation | Journal: To be Published Title: SARS-CoV main protease with N-terminal extension regulated by mutation on C-terminal domain Authors: Shi, J.H. / Song, J.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m3t.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m3t.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3t ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3t | HTTPS FTP |
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-Related structure data
Related structure data | 2h2zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33934.645 Da / Num. of mol.: 1 / Mutation: R298A Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: 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: 1.97 Å3/Da / Density % sol: 37.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2% PEG 6000, 0.1M Mes , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.081 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 6356 / % possible obs: 95.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Rsym value: 0.076 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 1.1 / Num. unique all: 644 / Rsym value: 0.228 / % possible all: 68.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 2H2Z Resolution: 2.9→33.1 Å / σ(F): 2
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Solvent computation | Bsol: 34.193 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 63.578 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→33.1 Å
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Refine LS restraints |
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