+Open data
-Basic information
Entry | Database: PDB / ID: 1q2w | ||||||
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Title | X-Ray Crystal Structure of the SARS Coronavirus Main Protease | ||||||
Components | 3C-like protease | ||||||
Keywords | HYDROLASE / SARS-CoV main protease / three domain protein (two antiparallel beta barrels / one alpha helical) | ||||||
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 / SARS-CoV-1 modulates host translation machinery / viral genome replication ...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 / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 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 / methylation / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Bonanno, J.B. / Fowler, R. / Gupta, S. / Hendle, J. / Lorimer, D. / Romero, R. / Sauder, J.M. / Wei, C.L. / Liu, E.T. / Burley, S.K. / Harris, T. | ||||||
Citation | Journal: New York Times / Year: 2003 Title: Company Says It Mapped Part of SARS Virus Authors: Bonanno, J.B. / Fowler, R. / Gupta, S. / Hendle, J. / Lorimer, D. / Romero, R. / Sauder, J.M. / Wei, C.L. / Liu, E.T. / Burley, S.K. / Harris, T. | ||||||
History |
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Remark 600 | heterogen 15% MPD was added to the crystals as a cryoprotectant. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q2w.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q2w.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q2w_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 1q2w_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1q2w_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1q2w_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/1q2w ftp://data.pdbj.org/pub/pdb/validation_reports/q2/1q2w | HTTPS FTP |
-Related structure data
Related structure data | 1lvoS 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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Details | Biological dimer represented in the asymmetric unit |
-Components
#1: Protein | Mass: 33987.730 Da / Num. of mol.: 2 / Fragment: Replicase polyprotein 1a residues 3241-3544 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome-related coronavirus Genus: Coronavirus / Gene: 1a / Plasmid: modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-MPD / ( | #3: 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: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: PEG 20K, sodium chloride, BME, methionine, glycerol, pH 6.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9198 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→26.3 Å / Num. all: 54757 / Num. obs: 54747 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7398 / Rsym value: 0.505 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on 1LVO Resolution: 1.86→5 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31 Å2 | |||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.213 Å / Luzzati d res low obs: 5 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å /
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