+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jjy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of KIBRA and beta-Dystroglycan | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14 | ||||||
Function / homology | ![]() Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape / regulation of hippo signaling ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape / regulation of hippo signaling / O-linked glycosylation / Signaling by Hippo / contractile ring / regulation of gastrulation / microtubule anchoring / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / dystrophin-associated glycoprotein complex / laminin-1 binding / response to denervation involved in regulation of muscle adaptation / basement membrane organization / positive regulation of myelination / regulation of epithelial to mesenchymal transition / skeletal muscle tissue regeneration / negative regulation of organ growth / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / photoreceptor ribbon synapse / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / angiogenesis involved in wound healing / commissural neuron axon guidance / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / axon regeneration / positive regulation of cell-matrix adhesion / structural constituent of muscle / negative regulation of MAPK cascade / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / negative regulation of hippo signaling / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / GABA-ergic synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / heart morphogenesis / laminin binding / tubulin binding / SH2 domain binding / negative regulation of cell migration / nuclear periphery / filopodium / morphogenesis of an epithelium / adherens junction / axon guidance / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / kinase binding / Regulation of expression of SLITs and ROBOs / ruffle membrane / Golgi lumen / cellular response to mechanical stimulus / protein transport / cell migration / lamellipodium / protein-macromolecule adaptor activity / virus receptor activity / actin binding / basolateral plasma membrane / postsynaptic membrane / collagen-containing extracellular matrix / positive regulation of MAPK cascade / molecular adaptor activity / transcription coactivator activity / cytoskeleton / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / calcium ion binding / protein-containing complex binding / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, Z. / Yang, Z. / Ji, Z. / Zhang, M. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j68SC ![]() 6jjwC ![]() 6jjxC ![]() 6jjzC ![]() 6jk0C ![]() 6jk1C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 16036.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein/peptide | Mass: 2298.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.53 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 15114 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 40 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 724 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6J68 Resolution: 2.298→40.571 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.48 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.298→40.571 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -94.2259 Å / Origin y: 65.4788 Å / Origin z: 127.1158 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |