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- PDB-4mh0: Selective activation of Epac1 and Epac2 -

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Basic information

Entry
Database: PDB / ID: 4mh0
TitleSelective activation of Epac1 and Epac2
Components
  • Rap guanine nucleotide exchange factor 4
  • Ras-related protein Rap-1b
KeywordsSIGNALING PROTEIN/GTP-BINDING PROTEIN / Guanine Nucleotide Exchange Factor / Nucleotide Binding / SIGNALING PROTEIN-GTP-BINDING PROTEIN complex
Function / homology
Function and homology information


Rap protein signal transduction / Integrin signaling / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of exocytosis / modification of postsynaptic structure / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation ...Rap protein signal transduction / Integrin signaling / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of exocytosis / modification of postsynaptic structure / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / calcium-ion regulated exocytosis / hormone secretion / negative regulation of synaptic vesicle exocytosis / Rap1 signalling / establishment of endothelial barrier / regulation of synaptic vesicle cycle / MET activates RAP1 and RAC1 / insulin secretion / regulation of establishment of cell polarity / azurophil granule membrane / small GTPase-mediated signal transduction / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / cAMP binding / cellular response to cAMP / lipid droplet / Integrin signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / hippocampal mossy fiber to CA3 synapse / guanyl-nucleotide exchange factor activity / small monomeric GTPase / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of insulin secretion / small GTPase binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / G protein activity / protein-macromolecule adaptor activity / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / Neutrophil degranulation / protein-containing complex binding / GTP binding / glutamatergic synapse / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1240 / Ras-related protein Rap1 / 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 / 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 ...Helicase, Ruva Protein; domain 3 - #1240 / Ras-related protein Rap1 / 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 / 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-like guanine nucleotide exchange factor / 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 domain superfamily / Ras guanine-nucleotide exchange factor, catalytic 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 / Small GTPase, Ras-type / small GTPase Ras family profile. / Jelly Rolls / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / RmlC-like jelly roll fold / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-HR4 / Ras-related protein Rap-1b / Rap guanine nucleotide exchange factor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRehmann, H.
CitationJournal: To be Published
Title: Selective activation of Epac1 and Epac2
Authors: Rehmann, H.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Rap guanine nucleotide exchange factor 4
R: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3655
Polymers98,2982
Non-polymers1,0673
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-16 kcal/mol
Surface area35550 Å2
MethodPISA
2
E: Rap guanine nucleotide exchange factor 4
R: Ras-related protein Rap-1b
hetero molecules

E: Rap guanine nucleotide exchange factor 4
R: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,73110
Polymers196,5974
Non-polymers2,1346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area9790 Å2
ΔGint-45 kcal/mol
Surface area67570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.758, 148.744, 225.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11E-1105-

HOH

21E-1109-

HOH

31E-1144-

HOH

41E-1177-

HOH

51E-1277-

HOH

61E-1297-

HOH

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Components

#1: Protein Rap guanine nucleotide exchange factor 4 / Exchange factor directly activated by cAMP 2 / Exchange protein directly activated by cAMP 2 / EPAC ...Exchange factor directly activated by cAMP 2 / Exchange protein directly activated by cAMP 2 / EPAC 2 / cAMP-dependent Rap1 guanine-nucleotide exchange factor / cAMP-regulated guanine nucleotide exchange factor II / cAMP-GEFII


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
#2: Protein Ras-related protein Rap-1b / GTP-binding protein smg p21B


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 ChemComp-HR4 / (2S,4aR,6R,7R,7aS)-6-{6-amino-8-[(4-fluorobenzyl)sulfanyl]-9H-purin-9-yl}-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide


Mass: 485.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17FN5O5PS2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 5.36 Å3/Da / Density % sol: 77.03 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 81301 / Num. obs: 81301 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 2.21 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CF6

3cf6


Resolution: 2.4→38.38 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.62 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28227 3975 4.9 %RANDOM
Rwork0.26563 ---
all0.26643 77325 --
obs0.26643 77325 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: 51.073 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--1.79 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 67 229 6534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9758685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3225770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83724.243304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.909151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.521543
X-RAY DIFFRACTIONr_chiral_restr0.0570.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214767
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3051.53865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56626265
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.53532559
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9874.52420
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 285 -
Rwork0.346 5491 -
obs--100 %

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