+
Open data
-
Basic information
Entry | Database: PDB / ID: 4mgk | ||||||
---|---|---|---|---|---|---|---|
Title | Selective activation of Epac1 and Epac2 | ||||||
![]() |
| ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 771.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 783.3 KB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mgiC ![]() 4mgyC ![]() 4mgzC ![]() 4mh0C ![]() 3cf6S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() ![]() |
---|---|
#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-CMP / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.24 Å3/Da / Density % sol: 76.51 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2009 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 56554 / Num. obs: 56554 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.03 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CF6 Resolution: 2.7→19.9 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.026 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 53.124 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.9 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
|