+Open data
-Basic information
Entry | Database: PDB / ID: 6xa6 | ||||||||||||
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Title | Crystal Structure of Human Scribble PDZ3:Vangl2 Complex | ||||||||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Cell polarity | ||||||||||||
Function / homology | Function and homology information cell migration involved in kidney development / neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / establishment of planar polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex ...cell migration involved in kidney development / neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / establishment of planar 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 / apical protein localization / non-motile cilium assembly / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / PCP/CE pathway / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / Wnt signaling pathway, planar cell polarity pathway / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / receptor clustering / heart looping / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / lateral plasma membrane / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / cell-cell junction / cell migration / positive regulation of type II interferon production / presynapse / lamellipodium / cell junction / basolateral plasma membrane / cell population proliferation / postsynaptic density / membrane => GO:0016020 / cadherin binding / positive regulation of apoptotic process / apical plasma membrane / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | How, J.Y. / Kvansakul, M. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Biochem.J. / Year: 2021 Title: Structural basis of the human Scribble-Vangl2 association in health and disease. Authors: How, J.Y. / Stephens, R.K. / Lim, K.Y.B. / 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 | 6xa6.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xa6.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xa6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/6xa6 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/6xa6 | HTTPS FTP |
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-Related structure data
Related structure data | 6xa7C 6xa8C 7jo7C 4wyuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10082.529 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: 920.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULK5 #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.8 and 66% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9357 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9357 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→37.08 Å / Num. obs: 15107 / % possible obs: 99.88 % / Redundancy: 27.6 % / Biso Wilson estimate: 34.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.36 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 5.54 / Num. unique obs: 1475 / CC1/2: 0.952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WYU Resolution: 1.95→37.08 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9974 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: 47.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→37.08 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 |
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