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Yorodumi- PDB-6w2a: 1.65 A resolution structure of SARS-CoV 3CL protease in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w2a | |||||||||
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Title | 1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j | |||||||||
Components | Replicase polyprotein 1a | |||||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / PROTEASE / severe acute respiratory syndrome coronavirus / SARS 3CL protease Inhhibitors / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | |||||||||
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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Human SARS coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | |||||||||
Authors | Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Rathnayake, A.D. / Zheng, J. / Kim, Y. / Nguyen, H.N. / Chang, K.O. / Groutas, W.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Transl Med / Year: 2020 Title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Authors: Rathnayake, A.D. / Zheng, J. / Kim, Y. / Perera, K.D. / Mackin, S. / Meyerholz, D.K. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Groutas, W.C. / Chang, K.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w2a.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w2a.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w2a_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6w2a_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6w2a_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 6w2a_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w2a ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w2a | HTTPS FTP |
-Related structure data
Related structure data | 6vgyC 6vgzC 6vh0C 6vh1C 6vh2C 6vh3C 6xmkC 5wkkS 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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Unit cell |
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-Components
#1: Protein | Mass: 34460.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Gene: 1a / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P0C6U8, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% (w/v) PEG 3350, 0.1 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 72975 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.6 / Num. measured all: 490396 / Scaling rejects: 7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WKK Resolution: 1.65→33.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 23.61 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→33.93 Å
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LS refinement shell |
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