+Open data
-Basic information
Entry | Database: PDB / ID: 8bia | |||||||||
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Title | Crystal structure of Scribble PDZ1 with PTHR | |||||||||
Components |
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Keywords | PROTEIN BINDING / Scribble / PTHR / PDZ domain / cell polarity | |||||||||
Function / homology | Function and homology information neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / parathyroid hormone receptor activity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / parathyroid hormone receptor activity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / synaptic vesicle targeting / 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 / G protein-coupled peptide receptor 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 / Class B/2 (Secretin family receptors) / negative regulation of mitotic cell cycle / osteoblast development / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of inositol phosphate biosynthetic process / positive regulation of receptor recycling / positive chemotaxis / bone mineralization / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / peptide hormone binding / CDC42 GTPase cycle / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cell maturation / synaptic vesicle endocytosis / immunological synapse / chondrocyte differentiation / bone resorption / signaling adaptor activity / skeletal system development / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / cell-cell adhesion / wound healing / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / positive regulation of type II interferon production / cell junction / cell-cell junction / cell migration / lamellipodium / presynapse / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / G alpha (s) signalling events / in utero embryonic development / receptor complex / cell population proliferation / cell surface receptor signaling pathway / postsynaptic density / cadherin binding / apical plasma membrane / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / glutamatergic synapse / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Stewart, B.Z. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide Authors: Stewart, B.Z. / Caria, S. / 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 | 8bia.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bia.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/8bia ftp://data.pdbj.org/pub/pdb/validation_reports/bi/8bia | HTTPS FTP |
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-Related structure data
Related structure data | 8b82C 8b87C 8b8oC 8b9tC 8bj0C 6mtvS 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: 12293.823 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 BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q14160 |
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#2: Protein/peptide | Mass: 1051.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03431 |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.72 % / Description: triangular diamond prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate pH 5.2, 43% PEG 300 |
-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 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→51.66 Å / Num. obs: 6472 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 56.57 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.4→2.486 Å / Num. unique obs: 623 / CC1/2: 0.891 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MTV Resolution: 2.4→51.63 Å / SU ML: 0.1752 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0619 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: 65.28 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→51.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.0246235025 Å / Origin y: 27.1692229986 Å / Origin z: -12.4512720899 Å
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Refinement TLS group | Selection details: all |