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- PDB-1o7f: CRYSTAL STRUCTURE OF THE REGULATORY DOMAIN OF EPAC2 -

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Basic information

Entry
Database: PDB / ID: 1o7f
TitleCRYSTAL STRUCTURE OF THE REGULATORY DOMAIN OF EPAC2
ComponentsCAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR
KeywordsREGULATION / EPAC2 / CAMP-GEF2 / CAMP / CAMPB BINDING DOAMIN / GEF / EXCHANGE FACTOR
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / cone cell pedicle / positive regulation of neuronal action potential / Integrin signaling / regulation of dendrite development / Rap1 signalling / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of synaptic vesicle cycle ...guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / cone cell pedicle / positive regulation of neuronal action potential / Integrin signaling / regulation of dendrite development / Rap1 signalling / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of synaptic vesicle cycle / hormone secretion / calcium-ion regulated exocytosis / regulation of exocytosis / negative regulation of synaptic transmission / insulin secretion / regulation of postsynapse organization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / small GTPase-mediated signal transduction / positive regulation of smooth muscle cell migration / brush border / excitatory synapse / photoreceptor outer segment / cAMP binding / photoreceptor inner segment / cAMP-mediated signaling / 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 / cilium / 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 / signal transduction / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. ...Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Rap guanine nucleotide exchange factor 4 / Rap guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 2.5 Å
AuthorsRehmann, H. / Prakash, B. / Wolf, E. / Rueppel, A. / De Rooij, J. / Bos, J.L. / Wittinghofer, A.
CitationJournal: 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. / De Rooij, J. / Bos, J.L. / Wittinghofer, A.
History
DepositionNov 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR


Theoretical massNumber of molelcules
Total (without water)53,2711
Polymers53,2711
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.429, 96.062, 103.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR


Mass: 53270.602 Da / Num. of mol.: 1
Fragment: CNMP-BINDING DOMAIN, DISHEVELLED-EGL-PLECKSTRIN (DEP), CNMB-BINDING DOMAIN, RESIDUES 1-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Z1P0, UniProt: Q9EQZ6*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 66 %
Crystal growpH: 7.5 / Details: 25 MM HEPES PH 7.5, 1M NA K PHOSPHATE, 10 MM DTE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMHEPES1reservoirpH7.5
3250 mM1reservoirNaH2PO4
4750 mM1reservoirK2HPO4
510 mMdithiothreitol1reservoir
640 mg/mlprotein1drop
21reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 23875 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 57.8 Å2 / Net I/σ(I): 24.4
Reflection shellResolution: 2.5→2.7 Å / Rmerge(I) obs: 0.017 / Mean I/σ(I) obs: 7.8 / % possible all: 92.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 151369 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 92.9 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
SnBphasing
SHARPphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 2.5→25 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2123814.59 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1204 5 %RANDOM
Rwork0.244 ---
obs0.244 23875 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3068 Å2 / ksol: 0.357018 e/Å3
Displacement parametersBiso mean: 63.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.69 Å20 Å20 Å2
2--1.77 Å20 Å2
3---4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 69 3437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 187 4.8 %
Rwork0.357 3728 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER-REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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