+Open data
-Basic information
Entry | Database: PDB / ID: 4mgz | ||||||
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Title | Selective activation of Epac1 and Epac2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN/GTP-BINDING PROTEIN / Guanine Nucleotide Exchange Factor / Nucleotide Binding / SIGNALING PROTEIN-GTP-BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information 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 / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / regulation of synaptic vesicle cycle / regulation of exocytosis / negative regulation of synaptic vesicle exocytosis / hormone secretion / calcium-ion regulated exocytosis / Rap1 signalling / establishment of endothelial barrier / negative regulation of synaptic transmission / MET activates RAP1 and RAC1 / insulin secretion / regulation of establishment of cell polarity / 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 / photoreceptor inner segment / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Integrin signaling / hippocampal mossy fiber to CA3 synapse / lipid droplet / small monomeric GTPase / G protein activity / guanyl-nucleotide exchange factor 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 / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / basolateral plasma membrane / growth cone / Ras protein signal transduction / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / dendritic spine / postsynaptic density / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Rehmann, H. | ||||||
Citation | Journal: To be Published Title: Selective activation of Epac1 and Epac2 Authors: Rehmann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mgz.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mgz.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mgz_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4mgz_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4mgz_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 4mgz_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/4mgz ftp://data.pdbj.org/pub/pdb/validation_reports/mg/4mgz | HTTPS FTP |
-Related structure data
Related structure data | 4mgiC 4mgkC 4mgyC 4mh0C 3cf6S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 79277.836 Da / Num. of mol.: 1 / Fragment: UNP residues 324-1011 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rapgef4, Cgef2, Epac2 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: Q9EQZ6 | ||||
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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.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: ptac / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P61224 | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 5.31 Å3/Da / Density % sol: 76.84 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2008 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07225 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 41504 / Num. obs: 41504 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3→3.1 Å / Mean I/σ(I) obs: 4.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CF6 Resolution: 3→35.85 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.846 / SU B: 13.584 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.494 / ESU R Free: 0.325 / 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: 50.664 Å2
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Refinement step | Cycle: LAST / Resolution: 3→35.85 Å
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