[English] 日本語
Yorodumi- PDB-5oak: Structure of the dmPar3 PDZ1 domain in complex with the dmPar6 PBM -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oak | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the dmPar3 PDZ1 domain in complex with the dmPar6 PBM | |||||||||
Components | Bazooka, isoform C,LD29223p | |||||||||
Keywords | PROTEIN BINDING / Cell polarity protein | |||||||||
Function / homology | Function and homology information spot adherens junction / follicle cell of egg chamber-cell adhesion / border follicle cell delamination / germ-band extension / Malpighian tubule development / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity ...spot adherens junction / follicle cell of egg chamber-cell adhesion / border follicle cell delamination / germ-band extension / Malpighian tubule development / RAC1 GTPase cycle / RHOV GTPase cycle / terminal branching, open tracheal system / subapical complex / establishment or maintenance of neuroblast polarity / branching involved in open tracheal system development / zonula adherens assembly / RHOU GTPase cycle / establishment of neuroblast polarity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / photoreceptor cell morphogenesis / Asymmetric localization of PCP proteins / oocyte anterior/posterior axis specification / establishment or maintenance of polarity of embryonic epithelium / oocyte microtubule cytoskeleton organization / muscle cell postsynaptic specialization / germarium-derived oocyte fate determination / asymmetric protein localization involved in cell fate determination / regulation of cellular localization / border follicle cell migration / negative regulation of filopodium assembly / establishment of apical/basal cell polarity / establishment of centrosome localization / asymmetric neuroblast division / zonula adherens / morphogenesis of a polarized epithelium / apical cortex / phosphatidic acid binding / apical protein localization / positive regulation of smoothened signaling pathway / establishment or maintenance of epithelial cell apical/basal polarity / centrosome cycle / positive regulation of filopodium assembly / apical junction complex / establishment of cell polarity / protein kinase inhibitor activity / bicellular tight junction / positive regulation of lamellipodium assembly / synapse assembly / phosphatidylinositol binding / adherens junction / protein localization / terminal bouton / microtubule cytoskeleton organization / cell cortex / cell adhesion / apical plasma membrane / cell cycle / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Bruekner, S.R. / Wiesner, S. | |||||||||
Funding support | Germany, 2items
| |||||||||
Citation | Journal: Sci Signal / Year: 2018 Title: Structural basis for the interaction between the cell polarity proteins Par3 and Par6. Authors: Renschler, F.A. / Bruekner, S.R. / Salomon, P.L. / Mukherjee, A. / Kullmann, L. / Schutz-Stoffregen, M.C. / Henzler, C. / Pawson, T. / Krahn, M.P. / Wiesner, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5oak.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5oak.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 5oak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/5oak ftp://data.pdbj.org/pub/pdb/validation_reports/oa/5oak | HTTPS FTP |
---|
-Related structure data
Related structure data | 2w4fS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12252.779 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: dmPar3 PDZ1 domain with N-terminal cloning artifact (GAMG) fused to a C-terminal Gly-Ser-linker followed by the dmPar6 PBM (VKDGVLHL) Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: baz, CG5055, Dmel_CG5055, par-6, CG5884, Dmel_CG5884 / Plasmid: pET M41 / Production host: Escherichia coli (E. coli) / References: UniProt: X2JFU8, UniProt: O97111 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris pH 6.5, 2 M Ammoniumsulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→40.959 Å / Num. obs: 43343 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.241 % / Biso Wilson estimate: 23.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.045 / Χ2: 0.97 / Net I/σ(I): 26.63 / Num. measured all: 443891 / Scaling rejects: 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W4F Resolution: 1.5→40.959 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.46
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.16 Å2 / Biso mean: 32.18 Å2 / Biso min: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→40.959 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
|