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Yorodumi- PDB-3wp0: Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wp0 | ||||||
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Title | Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide | ||||||
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 / Neurexins and neuroligins / L-leucine transport / beta-1 adrenergic receptor binding / regulation of Notch signaling pathway ...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 / Neurexins and neuroligins / L-leucine transport / beta-1 adrenergic receptor binding / regulation of Notch signaling pathway / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / myosin II binding / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / LGI-ADAM interactions / Golgi to plasma membrane transport / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / frizzled binding / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / dendritic spine organization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / positive regulation of dendrite morphogenesis / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical actin cytoskeleton organization / cortical actin cytoskeleton / cortical cytoskeleton / exocytosis / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / ionotropic glutamate receptor binding / dendrite cytoplasm / GTPase activator activity / synaptic membrane / cell periphery / PDZ domain binding / adherens junction / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / cell junction / cell-cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein phosphatase binding / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / cell division / intracellular membrane-bounded organelle / signaling receptor binding / glutamatergic synapse / synapse / dendrite / 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: 2.039 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 | 3wp0.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wp0.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 3wp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wp0_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 3wp0_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 3wp0_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3wp0_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wp0 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wp0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21414.131 Da / Num. of mol.: 1 / Fragment: UNP residues 533-713 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: 1862.139 Da / Num. of mol.: 1 / Fragment: UNP residues 640-654 / Source method: obtained synthetically / Details: LLGL2 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6P1M3 | ||
#3: Chemical | ChemComp-GOL / #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: 2.89 Å3/Da / Density % sol: 57.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.2M lithium chloride, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2012 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17523 / % possible obs: 99 % / 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: 2.039→42.041 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.714 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.039→42.041 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: 6
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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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