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Yorodumi- PDB-3wp1: Phosphorylation-dependent interaction between tumor suppressors D... -
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-Basic information
Entry | Database: PDB / ID: 3wp1 | ||||||
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Title | Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / MaGuk / Phosphorylation / Cell polarity / tumor suppressors / phosphorylation dependent | ||||||
Function / homology | Function and homology information establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / L-leucine transport / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding ...establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / L-leucine transport / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of Notch signaling pathway / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / proximal dendrite / AMPA glutamate receptor clustering / myosin II binding / cellular response to potassium ion / cerebellar mossy fiber / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / dendritic branch / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / neuron projection terminus / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / frizzled binding / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / cortical actin cytoskeleton organization / regulation of neuronal synaptic plasticity / cortical actin cytoskeleton / locomotory exploration behavior / cortical cytoskeleton / regulation of protein secretion / exocytosis / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / kinesin binding / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / GTPase activator activity / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / adherens junction / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / postsynapse / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / cell division / signaling receptor binding / intracellular membrane-bounded organelle / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å | ||||||
Authors | Zhu, J. / Shang, Y. / Wan, Q. / Xia, Y. / Chen, J. / Du, Q. / Zhang, M. | ||||||
Citation | Journal: Cell Res. / Year: 2014 Title: Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl Authors: Zhu, J. / Shang, Y. / Wan, Q. / Xia, Y. / Chen, J. / Du, Q. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wp1.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wp1.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wp1 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wp1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21414.131 Da / Num. of mol.: 1 / Fragment: UNP residues 531-713 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016 | ||
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#2: Protein/peptide | Mass: 2292.695 Da / Num. of mol.: 1 / Fragment: UNP residues 646-657 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6P1M3 | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.61 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97893 Å |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 8937 / Num. obs: 8915 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.804→42.865 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 26.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.275 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.804→42.865 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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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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