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Yorodumi- PDB-7qsa: Structural basis on the interaction of Scribble PDZ domains with ... -
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-Basic information
Entry | Database: PDB / ID: 7qsa | ||||||
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Title | Structural basis on the interaction of Scribble PDZ domains with the Tick Born encephalitis virus (TBEV) NS5 protein | ||||||
Components |
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Keywords | VIRAL PROTEIN / Tick Born encephalitis virus / TBEV / cell polarity / isothermal titration calorimetry / NS5 / PDZ / scribble | ||||||
Function / homology | Function and homology information neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / flavivirin / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / signaling adaptor activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / viral capsid / cell migration / cell-cell junction / positive regulation of type II interferon production / nucleoside-triphosphate phosphatase / presynapse / double-stranded RNA binding / cell junction / lamellipodium / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / basolateral plasma membrane / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cell population proliferation / postsynaptic density / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / cadherin binding / induction by virus of host autophagy / positive regulation of apoptotic process / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Tick-borne encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Javorsky, A. / Humbert, P.O. / Kvansakul, M. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.J. / Year: 2022 Title: Molecular basis of Tick Born encephalitis virus NS5 mediated subversion of apico-basal cell polarity signalling. Authors: Javorsky, A. / Humbert, P.O. / Kvansakul, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qsa.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qsa.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/7qsa ftp://data.pdbj.org/pub/pdb/validation_reports/qs/7qsa | HTTPS FTP |
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-Related structure data
Related structure data | 7qs9C 7qsbC 5vwiS 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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-Components
#1: Protein | Mass: 9758.154 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli (E. coli) / References: UniProt: Q14160 #2: Protein/peptide | | Mass: 931.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tick-borne encephalitis virus References: UniProt: Q01299, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase #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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium nitrate, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→31.02 Å / Num. obs: 12838 / % possible obs: 99.25 % / Redundancy: 12.2 % / Biso Wilson estimate: 42.61 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.1133 / Net I/σ(I): 7.58 |
Reflection shell | Resolution: 2.05→2.12 Å / Num. unique obs: 2401 / CC1/2: 0.51 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VWI Resolution: 2.02→31.02 Å / SU ML: 0.3246 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8951 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: 47.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→31.02 Å
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Refine LS restraints |
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LS refinement shell |
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