+Open data
-Basic information
Entry | Database: PDB / ID: 6jjy | ||||||
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Title | Crystal Structure of KIBRA and beta-Dystroglycan | ||||||
Components |
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Keywords | SIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14 | ||||||
Function / homology | Function and homology information 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 / contractile ring / Signaling by Hippo / 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 / photoreceptor ribbon synapse / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / myelination in peripheral nervous system / branching involved in salivary gland morphogenesis / node of Ranvier / costamere / commissural neuron axon guidance / angiogenesis involved in wound healing / response to muscle activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / axon regeneration / structural constituent of muscle / positive regulation of cell-matrix adhesion / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / negative regulation of MAPK cascade / negative regulation of hippo signaling / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / laminin binding / heart morphogenesis / SH2 domain binding / tubulin binding / nuclear periphery / negative regulation of cell migration / filopodium / axon guidance / morphogenesis of an epithelium / adherens junction / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / ruffle membrane / Regulation of expression of SLITs and ROBOs / kinase binding / Golgi lumen / cellular response to mechanical stimulus / cell migration / protein-macromolecule adaptor activity / protein transport / virus receptor activity / lamellipodium / actin binding / postsynaptic membrane / basolateral plasma membrane / collagen-containing extracellular matrix / positive regulation of MAPK cascade / transcription coactivator activity / molecular adaptor activity / cytoskeleton / negative regulation of cell population proliferation / external side of plasma membrane / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å | ||||||
Authors | Lin, Z. / Yang, Z. / Ji, Z. / Zhang, M. | ||||||
Citation | Journal: Elife / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jjy.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jjy.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jjy ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jjy | HTTPS FTP |
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-Related structure data
Related structure data | 6j68SC 6jjwC 6jjxC 6jjzC 6jk0C 6jk1C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 16036.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wwc1, Kiaa0869 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SXA9 | ||
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#2: Protein/peptide | Mass: 2298.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14118 | ||
#3: Chemical | #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: 4.48 Å3/Da / Density % sol: 72.53 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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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: -94.2259 Å / Origin y: 65.4788 Å / Origin z: 127.1158 Å
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Refinement TLS group | Selection details: ALL |