+Open data
-Basic information
Entry | Database: PDB / ID: 1u2c | ||||||
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Title | Crystal Structure of a-dystroglycan | ||||||
Components | Dystroglycan | ||||||
Keywords | PROTEIN BINDING / IG-like domain / S6 like fold | ||||||
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 / MIR / Resolution: 2.3 Å | ||||||
Authors | Bozic, D. / Sciandra, F. / Lamba, D. / Brancaccio, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Structure of the N-terminal Region of Murine Skeletal Muscle {alpha}-Dystroglycan Discloses a Modular Architecture Authors: Bozic, D. / Sciandra, F. / Lamba, D. / Brancaccio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u2c.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u2c.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 1u2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u2c ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u2c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26226.779 Da / Num. of mol.: 1 / Fragment: residues 58-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q62165 |
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#2: 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: 2.7 Å3/Da / Density % sol: 54.46 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 |
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Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→35.72 Å / Num. all: 11584 / Num. obs: 11584 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29 Å2 |
Reflection shell | Highest resolution: 2.3 Å / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→35.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 259321.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.5021 Å2 / ksol: 0.32933 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→35.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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