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Yorodumi- PDB-2l1c: Shc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l1c | ||||||
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Title | Shc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1) | ||||||
Components |
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Keywords | CELL ADHESION / Shc-PTB / integrin beta3 / cytoplasmic tail | ||||||
Function / homology | Function and homology information regulation of superoxide metabolic process / : / : / positive regulation of cell proliferation in bone marrow / ERBB2 signaling pathway / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration ...regulation of superoxide metabolic process / : / : / positive regulation of cell proliferation in bone marrow / ERBB2 signaling pathway / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / interleukin-2-mediated signaling pathway / XBP1(S) activates chaperone genes / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / neurotrophin TRKA receptor binding / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of epidermal growth factor-activated receptor activity / regulation of release of sequestered calcium ion into cytosol / cell-substrate junction assembly / interleukin-15-mediated signaling pathway / mesodermal cell differentiation / angiogenesis involved in wound healing / alphav-beta3 integrin-IGF-1-IGF1R complex / transmembrane receptor protein tyrosine kinase adaptor activity / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of Ras protein signal transduction / extracellular matrix binding / Interleukin-15 signaling / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / positive regulation of cell adhesion mediated by integrin / integrin complex / regulation of growth / Shc-EGFR complex / Interleukin-2 signaling / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / epidermal growth factor binding / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / smooth muscle cell migration / microvillus membrane / Syndecan interactions / negative chemotaxis / epidermal growth factor receptor binding / Signaling by ALK / leukocyte migration / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / IRE1-mediated unfolded protein response / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / Fc-epsilon receptor signaling pathway / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / Signaling by ALK fusions and activated point mutants / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / ECM proteoglycans / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of bone resorption / positive regulation of T cell migration / SHC-related events triggered by IGF1R / Integrin cell surface interactions / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Deshmukh, L. / Gorbatyuk, V. / Vinogradova, O. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Integrin {beta}3 phosphorylation dictates its complex with the Shc phosphotyrosine-binding (PTB) domain. Authors: Deshmukh, L. / Gorbatyuk, V. / Vinogradova, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l1c.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2l1c.ent.gz | 1000.8 KB | Display | PDB format |
PDBx/mmJSON format | 2l1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/2l1c ftp://data.pdbj.org/pub/pdb/validation_reports/l1/2l1c | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 23167.484 Da / Num. of mol.: 1 / Fragment: PTB domain (UNP residues 17-207) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHC1, hCG_1997126 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DV78, UniProt: P29353*PLUS |
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#2: Protein/peptide | Mass: 3284.377 Da / Num. of mol.: 1 / Fragment: UNP residues 762-788 / Source method: obtained synthetically Details: The peptide was chemically synthesized based on the sequence of the human integrin beta3 cytoplasmic tail (representing residues 736R-762G) References: UniProt: P05106 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.4 mM [U-99% 13C; U-99% 15N] Shc, 0.8 mM integrin beta3, 5 mM DTT, 50 mM sodium chloride, 50 mM sodium phosphate, 1 mM DSS, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: refinement in explicit water | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 4196 / NOE intraresidue total count: 1793 / NOE medium range total count: 1704 / NOE sequential total count: 699 / Hydrogen bond constraints total count: 166 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 80 / Conformers submitted total number: 15 |