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Open data
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Basic information
Entry | Database: PDB / ID: 4mgy | ||||||
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Title | Selective activation of Epac1 and Epac2 | ||||||
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![]() | SIGNALING PROTEIN/GTP-BINDING PROTEIN / Guanine Nucleotide Exchange Factor / Nucleotide Binding / SIGNALING PROTEIN-GTP-BINDING PROTEIN complex | ||||||
Function / homology | ![]() cone cell pedicle / Rap protein signal transduction / Integrin signaling / positive regulation of neuronal action potential / modification of postsynaptic structure / regulation of dendrite development / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion ...cone cell pedicle / Rap protein signal transduction / Integrin signaling / positive regulation of neuronal action potential / modification of postsynaptic structure / regulation of dendrite development / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / regulation of synaptic vesicle cycle / negative regulation of synaptic vesicle exocytosis / hormone secretion / calcium-ion regulated exocytosis / regulation of exocytosis / Rap1 signalling / establishment of endothelial barrier / negative regulation of synaptic transmission / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / insulin secretion / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of postsynapse organization / azurophil granule membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / excitatory synapse / photoreceptor outer segment / cAMP binding / cellular response to cAMP / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / hippocampal mossy fiber to CA3 synapse / photoreceptor inner segment / Integrin signaling / lipid droplet / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / establishment of localization in cell / positive regulation of protein secretion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / small GTPase binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / protein-macromolecule adaptor activity / growth cone / basolateral plasma membrane / cell population proliferation / Ras protein signal transduction / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / apical plasma membrane / axon / GTPase activity / neuronal cell body / glutamatergic synapse / dendrite / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rehmann, H. | ||||||
![]() | ![]() Title: Selective activation of Epac1 and Epac2 Authors: Rehmann, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.7 KB | Display | ![]() |
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Full document | ![]() | 841.5 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mgiC ![]() 4mgkC ![]() 4mgzC ![]() 4mh0C ![]() 3cf6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 79276.781 Da / Num. of mol.: 1 / Fragment: UNP residues 324-1011 / Mutation: K405Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 19020.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-H07 / ( |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.33 Å3/Da / Density % sol: 76.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M CITRATE, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2008 |
Radiation | Monochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 64657 / Num. obs: 64657 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.7 Å / Mean I/σ(I) obs: 2.92 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CF6 Resolution: 2.6→38.32 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.115 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.343 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→38.32 Å
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