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Yorodumi- PDB-7smv: Crystallization of feline coronavirus Mpro with GC376 reveals mec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7smv | |||||||||
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Title | Crystallization of feline coronavirus Mpro with GC376 reveals mechanism of inhibition | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / HYDROLASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity ...host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Feline coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Khan, M.B. / Lu, J. / Young, H.S. / Lemieux, M.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Front Chem / Year: 2022 Title: Crystallization of Feline Coronavirus M pro With GC376 Reveals Mechanism of Inhibition. Authors: Lu, J. / Chen, S.A. / Khan, M.B. / Brassard, R. / Arutyunova, E. / Lamer, T. / Vuong, W. / Fischer, C. / Young, H.S. / Vederas, J.C. / Lemieux, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7smv.cif.gz | 424.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7smv.ent.gz | 292.4 KB | Display | PDB format |
PDBx/mmJSON format | 7smv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/7smv ftp://data.pdbj.org/pub/pdb/validation_reports/sm/7smv | HTTPS FTP |
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-Related structure data
Related structure data | 7snaC 6wtmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.996722317058, -0.0190552806247, 0.0786226364277), (-0.0156873931542, -0.907890615245, -0.418913519055), (0.0793632684216, -0.418773837567, 0.904615909983)Vector: -67. ...NCS oper: (Code: given Matrix: (-0.996722317058, -0.0190552806247, 0.0786226364277), Vector: |
-Components
#1: Protein | Mass: 33141.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Feline coronavirus / Production host: Escherichia coli (E. coli) / References: UniProt: B0LJQ9 #2: Chemical | #3: 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: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→45.31 Å / Num. obs: 44939 / % possible obs: 99.9 % / Redundancy: 13.15 % / Biso Wilson estimate: 39.21 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.52 |
Reflection shell | Resolution: 1.93→1.999 Å / Num. unique obs: 4441 / CC1/2: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6wtm Resolution: 1.93→45.31 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1675 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 46.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→45.31 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.06506783193 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -34.270952022 Å / Origin y: -4.06504608099 Å / Origin z: -8.36144334681 Å
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Refinement TLS group | Selection details: all |