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Open data
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Basic information
Entry | Database: PDB / ID: 6jjz | ||||||
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Title | Crystal Structure of MAGI2 and Dendrin complex | ||||||
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![]() | SIGNALING PROTEIN / WW tandem / PY tandem / MAGI2 / Dendrin | ||||||
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 / dendritic spine membrane / 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 membrane / perikaryon / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / centrosome / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, Z. / Zhang, H. / Yang, Z. / Ji, Z. / Zhang, M. / Zhu, J. | ||||||
![]() | ![]() Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity. Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.4 KB | Display | ![]() |
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PDB format | ![]() | 80.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 472.1 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j68C ![]() 6jjwC ![]() 6jjxC ![]() 6jjyC ![]() 6jk0C ![]() 6jk1C ![]() 2ysdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 12089.212 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1843.966 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4.6 Details: 2.0-2.5M ammonium sulfate, 100mM sodium acetate (pH 4.6) |
-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: Mar 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 29381 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 44 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1465 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YSD Resolution: 1.65→27.917 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 27.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→27.917 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.2337 Å / Origin y: -5.2763 Å / Origin z: 13.4028 Å
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Refinement TLS group | Selection details: all |