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Yorodumi- PDB-2byv: Structure of the cAMP responsive exchange factor Epac2 in its aut... -
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-Basic information
Entry | Database: PDB / ID: 2byv | ||||||
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Title | Structure of the cAMP responsive exchange factor Epac2 in its auto- inhibited state | ||||||
Components | RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 | ||||||
Keywords | REGULATION / EPAC2 / CAMP-GEF2 / CAMP / CYCLIC NUCLEOTIDE / GEF / EXCHANGE FACTOR / AUTO-INHIBITION / CDC25 HOMOLOGY DOMAIN | ||||||
Function / homology | Function and homology information cone cell pedicle / Integrin signaling / positive regulation of neuronal action potential / regulation of dendrite development / Rap1 signalling / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of synaptic vesicle cycle / regulation of exocytosis / hormone secretion ...cone cell pedicle / Integrin signaling / positive regulation of neuronal action potential / regulation of dendrite development / Rap1 signalling / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of synaptic vesicle cycle / regulation of exocytosis / hormone secretion / calcium-ion regulated exocytosis / negative regulation of synaptic transmission / insulin secretion / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of postsynapse organization / positive regulation of smooth muscle cell migration / brush border / excitatory synapse / photoreceptor outer segment / cAMP binding / photoreceptor inner segment / hippocampal mossy fiber to CA3 synapse / guanyl-nucleotide exchange factor activity / positive regulation of protein secretion / 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 / protein-macromolecule adaptor activity / growth cone / basolateral plasma membrane / Ras protein signal transduction / dendritic spine / postsynaptic density / apical plasma membrane / axon / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / protein-containing complex / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rehmann, H. / Wittinghofer, A. / Bos, J.L. | ||||||
Citation | 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. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Structure and Regulation of the Camp Binding Domains of Epac2 Authors: Rehmann, H. / Prakash, B. / Wolf, E. / Rueppel, A. / Derooij, 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 | 2byv.cif.gz | 193.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2byv.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 2byv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2byv ftp://data.pdbj.org/pub/pdb/validation_reports/by/2byv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 114150.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX4T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CK600K / References: UniProt: Q9EQZ6 |
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#2: 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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | pH: 7.5 Details: 100 MM BISTRISPROPANE7.5, 200 MM NANO3, 12% PEG 3350, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976269 |
Detector | Detector: CCD / Date: Dec 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976269 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 35428 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / % possible all: 96.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O7F, PDB ENTRY 1BKD Resolution: 2.7→29.88 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 14.86 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.885 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESDIUES 1-14, 171-178, 465-476, 614-641, 725-731, 992-993 ARE DISORDERED
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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: 62.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.88 Å
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Refine LS restraints |
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