+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bia | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Scribble PDZ1 with PTHR | |||||||||
![]() |
| |||||||||
![]() | PROTEIN BINDING / Scribble / PTHR / PDZ domain / cell polarity | |||||||||
Function / homology | ![]() extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / parathyroid hormone receptor activity / 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 / parathyroid hormone receptor activity / 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 / 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 / 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) / osteoblast development / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of inositol phosphate biosynthetic process / positive regulation of receptor recycling / positive chemotaxis / bone mineralization / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / chondrocyte differentiation / signaling adaptor activity / cell maturation / bone resorption / Asymmetric localization of PCP proteins / skeletal system development / neural tube closure / adherens junction / wound healing / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell adhesion / intracellular calcium ion homeostasis / : / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / basolateral plasma membrane / in utero embryonic development / cell population proliferation / postsynaptic density / cell surface receptor signaling pathway / receptor complex / cadherin binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / protein kinase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stewart, B.Z. / Kvansakul, M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b82C ![]() 8b87C ![]() 8b8oC ![]() 8b9tC ![]() 8bj0C ![]() 6mtvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12293.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1051.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.72 % / Description: triangular diamond prism |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.0246235025 Å / Origin y: 27.1692229986 Å / Origin z: -12.4512720899 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |