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- PDB-7ykh: Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ykh | ||||||
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Title | Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide | ||||||
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![]() | PEPTIDE BINDING PROTEIN / MAGI2 / PDZ0-GK / SAPAP1 / GBR2 / phosphorylated peptide | ||||||
Function / homology | ![]() structural constituent of postsynaptic specialization / extrinsic component of postsynaptic membrane / type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / positive regulation of synaptic vesicle clustering / slit diaphragm / beta-1 adrenergic receptor binding / structural constituent of postsynaptic density / activin receptor binding ...structural constituent of postsynaptic specialization / extrinsic component of postsynaptic membrane / type II activin receptor binding / neuroligin clustering involved in postsynaptic membrane assembly / podocyte development / positive regulation of synaptic vesicle clustering / slit diaphragm / beta-1 adrenergic receptor binding / structural constituent of postsynaptic density / activin receptor binding / nerve growth factor signaling pathway / clathrin-dependent endocytosis / SMAD protein signal transduction / negative regulation of activin receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synaptic membrane adhesion / ciliary base / receptor clustering / SMAD binding / kinesin binding / positive regulation of phosphoprotein phosphatase activity / positive regulation of receptor internalization / photoreceptor outer segment / GABA-ergic synapse / bicellular tight junction / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / centriole / photoreceptor inner segment / negative regulation of cell migration / cellular response to nerve growth factor stimulus / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / late endosome / postsynaptic density / negative regulation of cell population proliferation / centrosome / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / signal transduction / protein-containing complex / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, M. / Lin, L. / Zhu, J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Phosphorylation-dependent recognition of diverse protein targets by the cryptic GK domain of MAGI MAGUKs. Authors: Zhang, M. / Cao, A. / Lin, L. / Chen, Y. / Shang, Y. / Wang, C. / Zhang, M. / Zhu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.3 KB | Display | ![]() |
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Full document | ![]() | 477.3 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ykfC ![]() 7ykgC ![]() 7ykiC ![]() 2eehS ![]() 5ypoS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25982.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1702.823 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 3350, 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 14863 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.107 / Χ2: 2.186 / Net I/σ(I): 8.8 / Num. measured all: 108108 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2EEH,5YPO Resolution: 2.5→40.609 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.61 Å2 / Biso mean: 48.16 Å2 / Biso min: 26.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→40.609 Å
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Refine LS restraints |
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LS refinement shell |
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