[English] 日本語
Yorodumi- PDB-8b82: Crystal structure of Scribble PDZ1 with human papillomavirus stra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b82 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide | |||||||||
Components |
| |||||||||
Keywords | PROTEIN BINDING / Scribble / human papillomavirus / E6 / PDZ domain / cell polarity | |||||||||
Function / homology | Function and homology information extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / 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 ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / 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 / 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 / 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 / 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 / PDZ domain binding / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / lamellipodium / cell junction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 / virus-mediated perturbation of host defense response / negative regulation of DNA-templated transcription / DNA-templated transcription / glutamatergic synapse / host cell nucleus / DNA binding / zinc ion binding / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human papillomavirus type 18 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Stewart, B.Z. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8b82.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8b82.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 8b82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b82_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8b82_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 8b82_validation.xml.gz | 11 KB | Display | |
Data in CIF | 8b82_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/8b82 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/8b82 | HTTPS FTP |
-Related structure data
Related structure data | 8b87C 8b8oC 8b9tC 8biaC 8bj0C 6mtvS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12293.823 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 BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q14160 #2: Protein/peptide | Mass: 1345.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 18 / References: UniProt: P06463 #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % / Description: Rod |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 15% PEG 4000, 0.05 M Ammonium Sulfate / PH range: 8 / Temp details: 293.15 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.74 Å / Num. obs: 5671 / % possible obs: 99.23 % / Redundancy: 12.7 % / Biso Wilson estimate: 47.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1381 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.5239 / Num. unique obs: 560 / CC1/2: 0.964 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MTV Resolution: 2.8→49.74 Å / SU ML: 0.3488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.121 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.31 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.74 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -13.3072185206 Å / Origin y: 17.2103366331 Å / Origin z: -15.7530182633 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |