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Yorodumi- PDB-9ax9: Crystal Structure of Enterovirus 68 3C Protease C147A Mutant with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ax9 | ||||||
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Title | Crystal Structure of Enterovirus 68 3C Protease C147A Mutant with 3B3C peptide at 2.00 Angstroms | ||||||
Components |
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Keywords | VIRAL PROTEIN / HYDROLASE / PROTEASE / ENTEROVIRUS / 3C PROTEIN / EV68 / INHIBITOR | ||||||
Function / homology | Function and homology information : / RNA-protein covalent cross-linking / : / : / picornain 2A / ribonucleoside triphosphate phosphatase activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / RNA-protein covalent cross-linking / : / : / picornain 2A / ribonucleoside triphosphate phosphatase activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / endocytosis involved in viral entry into host cell / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human enterovirus D68 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Azzolino, V.N. / Shaqra, A.M. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Viruses / Year: 2024 Title: Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance. Authors: Azzolino, V.N. / Shaqra, A.M. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ax9.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ax9.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 9ax9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ax9_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 9ax9_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 9ax9_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 9ax9_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/9ax9 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9ax9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20083.779 Da / Num. of mol.: 2 / Mutation: C147A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human enterovirus D68 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2K8BQT2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #2: Protein/peptide | | Mass: 599.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human enterovirus D68 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #3: Water | ChemComp-HOH / | Has protein modification | N | |
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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: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M BisTris Propane 0.2M Potassium Thiocyanate PEG3350 12-30% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→31.83 Å / Num. obs: 21924 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 32.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.041 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2200 / CC1/2: 0.942 / Rpim(I) all: 0.163 / Rrim(I) all: 0.231 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.19 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.5573 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.19 Å
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Refine LS restraints |
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LS refinement shell |
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