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- PDB-4f7z: Conformational dynamics of exchange protein directly activated by cAMP -

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Basic information

Entry
Database: PDB / ID: 4f7z
TitleConformational dynamics of exchange protein directly activated by cAMP
ComponentsRap guanine nucleotide exchange factor 4
KeywordsEXOCYTOSIS / cyclic nucleotide / GEF / exchange factor / regulation / 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 exocytosis / regulation of synaptic vesicle cycle / 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 exocytosis / regulation of synaptic vesicle cycle / calcium-ion regulated exocytosis / hormone secretion / 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 / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating 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
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 ...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 / 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: 2.6 Å
AuthorsWhite, M.A. / Tsalkova, T.N. / Mei, F.C. / Liu, T. / Woods, V.L. / Cheng, X.
CitationJournal: Plos One / Year: 2012
Title: Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP.
Authors: White, M.A. / Li, S. / Tsalkova, T. / Mei, F.C. / Liu, T. / Woods, V.L. / Cheng, X.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 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
A: Rap guanine nucleotide exchange factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7058
Polymers114,0601
Non-polymers6457
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.720, 95.350, 181.840
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 / Epac2 / Exchange factor directly activated by cAMP 2 / Exchange protein directly activated by cAMP ...Epac2 / 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: 114060.438 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: F435G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rapgef4, Cgef2, Epac2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQZ6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS ISOFORM 3 OF RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 (Q9EQZ6-3), IN WHICH UNP RESIDUES ...PROTEIN IS ISOFORM 3 OF RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 (Q9EQZ6-3), IN WHICH UNP RESIDUES 180-197 ARE MISSING.

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Bis-Tris propane, pH 7.5, 200 mM sodium chloride, 1.3 M ammonium sulfate, 6% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976269
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976269 Å / Relative weight: 1
ReflectionResolution: 2.6→45.46 Å / Num. obs: 37453 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 34
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2488 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYV

2byv


Resolution: 2.6→45.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2279149.98 / Data cutoff low absF: 0 / Isotropic thermal model: VARIABLE / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1889 5 %THICK SHELLS
Rwork0.222 ---
obs0.222 35539 98.2 %-
all-37428 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1178 Å2 / ksol: 0.348488 e/Å3
Displacement parametersBiso mean: 78.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 42 17 7666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
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: 2.6→2.64 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 131 7.4 %
Rwork0.345 1630 -
obs-1761 93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_pmb.paramprotein_pmb.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5carbohydrate.param

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