+Open data
-Basic information
Entry | Database: PDB / ID: 3cf6 | ||||||
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Title | Structure of Epac2 in complex with cyclic-AMP and Rap | ||||||
Components |
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Keywords | SIGNALING PROTEIN/GTP-BINDING PROTEIN / EPAC / RAPGEF4 / RAP / RAP1B / CAMP / SP-CAMPS / GEF / GUNANINE NUCLEOTIDE EXCHANGE FACTOR / G-PROTEIN / GTP-BINDING / NUCLEOTIDE-BINDING / SIGNALING PROTEIN REGULATOR-GTP-BINDING PROTEIN COMPLEX / SIGNALING PROTEIN-GTP-BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity ...Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / cellular response to cAMP / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / 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: 2.2 Å | ||||||
Authors | Rehmann, H. / Arias-Palomo, E. / Hadders, M.A. / Schwede, F. / Llorca, O. / Bos, J.L. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B. Authors: Holger Rehmann / Ernesto Arias-Palomo / Michael A Hadders / Frank Schwede / Oscar Llorca / Johannes L Bos / Abstract: Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell ...Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain. #1: Journal: Nature / Year: 2006 Title: Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state Authors: Rehmann, H. / Das, J. / Knipscheer, P. / Wittinghofer, A. / Bos, J.L. #2: Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure and regulation of the cAMP-binding domains of Epac2 Authors: Rehmann, H. / Prakash, B. / Wolf, E. / Rueppel, A. / de Rooij, J. / Bos, J.L. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cf6.cif.gz | 178 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cf6.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/3cf6 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cf6 | HTTPS FTP |
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-Related structure data
Related structure data | 1510C 1bkdS 2byvS 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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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 306-993 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: GST fusion / Gene: Rapgef4 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: A2ASW3 | ||||
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#2: Protein | Mass: 19020.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B / 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: 5.352371 Å3/Da / Density % sol: 77.019531 % |
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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: 0.9732 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007 / Details: mirror |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 104773 / Num. obs: 102111 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.62 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.96 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2byv, pdb entry 1BKD Resolution: 2.2→48.56 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 48.187 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.56 Å
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Refine LS restraints |
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