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- PDB-2byv: Structure of the cAMP responsive exchange factor Epac2 in its aut... -

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Basic information

Entry
Database: PDB / ID: 2byv
TitleStructure of the cAMP responsive exchange factor Epac2 in its auto- inhibited state
ComponentsRAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4
KeywordsREGULATION / EPAC2 / CAMP-GEF2 / CAMP / CYCLIC NUCLEOTIDE / GEF / EXCHANGE FACTOR / AUTO-INHIBITION / CDC25 HOMOLOGY DOMAIN
Function / homology
Function and homology information


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 ...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 / positive regulation of smooth muscle cell migration / brush border / excitatory synapse / photoreceptor outer segment / cAMP binding / hippocampal mossy fiber to CA3 synapse / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / positive regulation of protein secretion / 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 / protein-macromolecule adaptor activity / growth cone / basolateral plasma membrane / Ras protein signal transduction / dendritic spine / postsynaptic density / apical plasma membrane / axon / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex binding / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / 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. ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ubiquitin-like (UB roll) / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rap guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRehmann, 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
DepositionAug 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4


Theoretical massNumber of molelcules
Total (without water)114,1511
Polymers114,1511
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.406, 97.038, 172.101
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 RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 / CAMP-REGULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR II / CAMP-GEFII / EXCHANGE FACTOR DIRECTLY ...CAMP-REGULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR II / CAMP-GEFII / EXCHANGE FACTOR DIRECTLY ACTIVATED BY CAMP 2 / EPAC 2 / CAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR


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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5
Details: 100 MM BISTRISPROPANE7.5, 200 MM NANO3, 12% PEG 3350, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976269
DetectorDetector: CCD / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976269 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O7F, PDB ENTRY 1BKD

1o7f

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
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1791 5 %RANDOM
Rwork0.245 ---
obs0.248 34014 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---1.64 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 0 66 7430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.951.95810166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76323.95357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.602151334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5671554
X-RAY DIFFRACTIONr_chiral_restr0.0650.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025641
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.23179
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.25136
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.341.54751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60827430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4433119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.754.52736
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 130
Rwork0.308 2462

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