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- PDB-6h7e: GEF regulatory domain -

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Basic information

Entry
Database: PDB / ID: 6h7e
TitleGEF regulatory domain
ComponentscDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3
KeywordsSTRUCTURAL PROTEIN / GEF / cAMP / regulatory / Membrane binding domain / EPAC
Function / homology
Function and homology information


negative regulation of syncytium formation by plasma membrane fusion / : / positive regulation of syncytium formation by plasma membrane fusion / positive regulation of protein acetylation / Rap protein signal transduction / Rap1 signalling / establishment of endothelial barrier / small GTPase-mediated signal transduction / microvillus / cAMP-mediated signaling ...negative regulation of syncytium formation by plasma membrane fusion / : / positive regulation of syncytium formation by plasma membrane fusion / positive regulation of protein acetylation / Rap protein signal transduction / Rap1 signalling / establishment of endothelial barrier / small GTPase-mediated signal transduction / microvillus / cAMP-mediated signaling / endomembrane system / cAMP binding / cellular response to cAMP / positive regulation of stress fiber assembly / Integrin signaling / guanyl-nucleotide exchange factor activity / positive regulation of protein export from nucleus / filopodium / Regulation of insulin secretion / positive regulation of GTPase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of angiogenesis / lamellipodium / positive regulation of peptidyl-serine phosphorylation / angiogenesis / adaptive immune response / protein domain specific binding / signal transduction / extracellular exosome / membrane / plasma membrane
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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3 / Rap guanine nucleotide exchange factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFerrandez, Y. / Cherfils, J. / Peurois, F.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: Nat Commun / Year: 2023
Title: Membranes prime the RapGEF EPAC1 to transduce cAMP signaling.
Authors: Sartre, C. / Peurois, F. / Ley, M. / Kryszke, M.H. / Zhang, W. / Courilleau, D. / Fischmeister, R. / Ambroise, Y. / Zeghouf, M. / Cianferani, S. / Ferrandez, Y. / Cherfils, J.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3
B: cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4246
Polymers60,5732
Non-polymers8514
Water2,432135
1
A: cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7123
Polymers30,2871
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7123
Polymers30,2871
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.698, 105.617, 160.556
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-570-

HOH

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Components

#1: Protein cDNA FLJ56134, highly similar to Rap guanine nucleotide exchange factor 3


Mass: 30286.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B7Z5J6, UniProt: O95398*PLUS
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS propane; pH 6.5 200 mM Sodium Potassium phosphate

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Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→88.24 Å / Num. obs: 180358 / % possible obs: 99.4 % / Redundancy: 6.7 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.3→2.39 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→88.237 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1548 5.04 %
Rwork0.1946 --
obs0.1966 30684 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→88.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 54 135 4111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064125
X-RAY DIFFRACTIONf_angle_d0.8775592
X-RAY DIFFRACTIONf_dihedral_angle_d16.9912472
X-RAY DIFFRACTIONf_chiral_restr0.051628
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.30911450.29072590X-RAY DIFFRACTION99
2.3742-2.45910.29731420.26062651X-RAY DIFFRACTION98
2.4591-2.55760.27081860.24332547X-RAY DIFFRACTION99
2.5576-2.6740.32171450.252648X-RAY DIFFRACTION99
2.674-2.8150.31791200.24352660X-RAY DIFFRACTION99
2.815-2.99130.29441440.23322656X-RAY DIFFRACTION99
2.9913-3.22230.26761470.20072632X-RAY DIFFRACTION99
3.2223-3.54660.2375990.19032705X-RAY DIFFRACTION100
3.5466-4.05980.20261610.16982638X-RAY DIFFRACTION100
4.0598-5.11490.18091430.14732675X-RAY DIFFRACTION100
5.1149-88.30220.19691160.17562734X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.036 Å / Origin y: -28.4623 Å / Origin z: 47.5518 Å
111213212223313233
T0.3633 Å2-0.0406 Å20.002 Å2-0.3275 Å2-0.0114 Å2--0.3437 Å2
L0.591 °2-0.1912 °2-0.4162 °2-0.3309 °20.1314 °2--1.0052 °2
S0.0364 Å °0.218 Å °0.0107 Å °-0.1977 Å °0.0244 Å °-0.0566 Å °0.0189 Å °-0.0431 Å °-0.0622 Å °
Refinement TLS groupSelection details: all

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