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Yorodumi- PDB-3m3s: Crystal structure of SARS-COV main protease Asn214Ala mutant with... -
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-Basic information
Entry | Database: PDB / ID: 3m3s | ||||||
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Title | Crystal structure of SARS-COV main protease Asn214Ala mutant with authorize N-terminus | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE / SARS coronavirus protease N214A mutation | ||||||
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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery ...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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / 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 / 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 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 / methylation / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shi, J.H. / Song, J.X. | ||||||
Citation | Journal: To be Published Title: Dynamical Inactivation of the Catalytic Machinery of the SARS-CoV 3C-Like Protease as Triggered by the N214A Mutation on the Extra 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 | 3m3s.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m3s.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 3m3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3s ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3s | 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: 33833.613 Da / Num. of mol.: 2 / Mutation: N214A Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Gene: main protease / 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 #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: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→66.678 Å / Num. all: 29514 / Num. obs: 29494 / % possible obs: 99.9 % / Redundancy: 5.73 % / Rmerge(I) obs: 0.111 / Rsym value: 0.086 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.4269 / Mean I/σ(I) obs: 1.95 / Num. unique all: 3511 / Rsym value: 0.5049 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 2H2Z Resolution: 2.3→66.478 Å / SU ML: 0.34 / σ(F): 0.09 / Phase error: 26.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.675 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.167 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→66.478 Å
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Refine LS restraints |
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LS refinement shell |
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