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

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Basic information

Entry
Database: PDB / ID: 4mgy
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


cone cell pedicle / Rap protein signal transduction / positive regulation of neuronal action potential / Integrin signaling / modification of postsynaptic structure / regulation of dendrite development / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion ...cone cell pedicle / Rap protein signal transduction / positive regulation of neuronal action potential / Integrin signaling / modification of postsynaptic structure / regulation of dendrite development / Rap1 signalling / regulation of cell junction assembly / Regulation of insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of integrin activation / negative regulation of calcium ion-dependent exocytosis / regulation of exocytosis / regulation of synaptic vesicle cycle / calcium-ion regulated exocytosis / negative regulation of synaptic vesicle exocytosis / hormone secretion / Rap1 signalling / establishment of endothelial barrier / negative regulation of synaptic transmission / MET activates RAP1 and RAC1 / insulin secretion / regulation of establishment of cell polarity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / azurophil granule membrane / regulation of postsynapse organization / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / excitatory synapse / photoreceptor outer segment / cAMP binding / cellular response to cAMP / photoreceptor inner segment / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Integrin signaling / hippocampal mossy fiber to CA3 synapse / lipid droplet / small monomeric GTPase / guanyl-nucleotide exchange factor activity / establishment of localization in cell / positive regulation of protein secretion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein activity / small GTPase 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 / GDP binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / protein-macromolecule adaptor activity / growth cone / basolateral plasma membrane / Ras protein signal transduction / cell population proliferation / dendritic spine / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / apical plasma membrane / axon / GTPase activity / neuronal cell body / glutamatergic synapse / dendrite / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / 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-H07 / 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: 2.6 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 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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

Downloads & links

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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)98,8794
Polymers98,2972
Non-polymers5822
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-17 kcal/mol
Surface area35280 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)197,7588
Polymers196,5954
Non-polymers1,1644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area10050 Å2
ΔGint-46 kcal/mol
Surface area66800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.592, 145.195, 229.991
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-1112-

HOH

21E-1124-

HOH

31E-1199-

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: 79276.781 Da / Num. of mol.: 1 / Fragment: UNP residues 324-1011 / Mutation: K405Q
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-H07 / (2S,4aR,6R,7R,7aR)-6-{6-amino-8-[(4-chlorophenyl)sulfanyl]-9H-purin-9-yl}-7-methoxytetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-2-ol 2-oxide


Mass: 485.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17ClN5O6PS
#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.: 231 / 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: 5.33 Å3/Da / Density % sol: 76.94 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Silicon 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 64657 / Num. obs: 64657 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 2.92 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CF6

3cf6


Resolution: 2.6→38.32 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.115 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26979 3140 4.9 %RANDOM
Rwork0.2517 ---
all0.25257 61517 --
obs0.25257 61517 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: 42.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.15 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 36 231 6505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9698633
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5675770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57124.262305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.251151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7551543
X-RAY DIFFRACTIONr_chiral_restr0.0580.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214751
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_it0.2871.53865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.53426265
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.49332524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8974.52368
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 244 -
Rwork0.321 4505 -
obs--100 %

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