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Yorodumi- PDB-7qtp: Structural biology of the NS1 avian influenza protein subversion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qtp | ||||||
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Title | Structural biology of the NS1 avian influenza protein subversion on the Scribble cell polarity module | ||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza A virus / bird-flu / H5N1 / cell polarity / isothermal titration calorimetry / NS1 / PDZ / scribble | ||||||
Function / homology | Function and homology information extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / 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 ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / symbiont-mediated suppression of host mRNA processing / 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 / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / protein serine/threonine kinase inhibitor activity / 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 / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / host cell nucleus / RNA binding / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) H5N1 subtype (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Javorsky, A. / Humbert, P.O. / Kvansakul, M. | ||||||
Funding support | 1items
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Citation | Journal: Viruses / Year: 2022 Title: Structural Basis of the Avian Influenza NS1 Protein Interactions with the Cell Polarity Regulator Scribble. 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 | 7qtp.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qtp.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qtp_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 7qtp_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 7qtp_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 7qtp_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/7qtp ftp://data.pdbj.org/pub/pdb/validation_reports/qt/7qtp | HTTPS FTP |
-Related structure data
Related structure data | 7qtoC 7qtuC 5vwcS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12380.901 Da / Num. of mol.: 1 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 |
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#2: Protein/peptide | Mass: 1165.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) H5N1 subtype (virus) / References: UniProt: Q6B3P2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 2.5M Ammonium nitrate, 0.1M Sodium acetate trihydrate pH 4.6 |
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-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: Mar 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.54 Å / Num. obs: 6533 / % possible obs: 99.54 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.88 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05011 / Net I/σ(I): 17.74 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.23 / Num. unique obs: 627 / CC1/2: 0.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VWC Resolution: 1.9→38.54 Å / SU ML: 0.2791 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.5508 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: 48.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→38.54 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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