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Yorodumi- PDB-5n30: Crystal structure of the V72I mutant of the mouse alpha-Dystrogly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n30 | |||||||||
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Title | Crystal structure of the V72I mutant of the mouse alpha-Dystroglycan N-terminal region | |||||||||
Components | Dystroglycan | |||||||||
Keywords | CELL ADHESION / Dystroglycan Cell Adhesion Laminin Binding | |||||||||
Function / homology | Function and homology information O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / contractile ring / Regulation of expression of SLITs and ROBOs / regulation of gastrulation / microtubule anchoring ...O-linked glycosylation / dystroglycan complex / nerve maturation / muscle attachment / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / contractile ring / Regulation of expression of SLITs and ROBOs / 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 / photoreceptor ribbon synapse / dystroglycan binding / cellular response to cholesterol / nerve development / vinculin binding / 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 / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / cellular response to organic cyclic compound / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / laminin binding / Schwann cell development / 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 / cellular response to mechanical stimulus / cell-cell junction / protein transport / virus receptor activity / lamellipodium / actin binding / heart development / postsynapse / postsynaptic membrane / basolateral plasma membrane / cytoskeleton / membrane raft / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / protein-containing complex binding / cell surface / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Cassetta, A. / Covaceuszach, S. / Brancaccio, A. / Sciandra, F. / Bozzi, M. / Bigotti, M.G. / Konarev, P.V. | |||||||||
Funding support | United Kingdom, France, 2items
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Citation | Journal: PLoS ONE / Year: 2017 Title: The effect of the pathological V72I, D109N and T190M missense mutations on the molecular structure of alpha-dystroglycan. Authors: Covaceuszach, S. / Bozzi, M. / Bigotti, M.G. / Sciandra, F. / Konarev, P.V. / Brancaccio, A. / Cassetta, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n30.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n30.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/5n30 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/5n30 | HTTPS FTP |
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-Related structure data
Related structure data | 5n4hC 1u2cS 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: 28312.236 Da / Num. of mol.: 1 / Mutation: V72I R166H Source method: isolated from a genetically manipulated source Details: V72i MUTANT / Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Skeletal Muscle / Gene: Dag1, Dag-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q62165 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #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: 2.5 Å3/Da / Density % sol: 50.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Cross streak-Seeding (from D109N alpha-DG mutant) 1 muL protein solution + 1 muL precipitant Seeding after 3-6 days of equilibration Protein Solution: (5 mg / mL protein, 25 mM Tris, 150 mM ...Details: Cross streak-Seeding (from D109N alpha-DG mutant) 1 muL protein solution + 1 muL precipitant Seeding after 3-6 days of equilibration Protein Solution: (5 mg / mL protein, 25 mM Tris, 150 mM NaCl, pH 7.5) Precipitant: 0.8 M citrate buffer, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2016 / Details: Pt-coated toroidal mirror |
Radiation | Monochromator: DOUBLE CRYSTAL Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36 Å / Num. obs: 25641 / % possible obs: 99.9 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.106 / Net I/σ(I): 15.84 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.306 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2530 / CC1/2: 0.862 / Rrim(I) all: 1.362 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U2C Resolution: 1.8→35.905 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.905 Å
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Refine LS restraints |
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LS refinement shell |
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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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