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- PDB-2b3a: Solution structure of the Ras-binding domain of the Ral Guanosine... -

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Basic information

Entry
Database: PDB / ID: 2b3a
TitleSolution structure of the Ras-binding domain of the Ral Guanosine Dissociation Stimulator
ComponentsRal guanine nucleotide dissociation stimulator
KeywordsSIGNALING PROTEIN / Ras binding domain / ubiquitin fold / signal transduction / automatically solved / AUREMOL
Function / homology
Function and homology information


GTPase regulator activity / brush border / p38MAPK events / guanyl-nucleotide exchange factor activity / RAF/MAP kinase cascade / Ras protein signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) 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 ...Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ral guanine nucleotide dissociation stimulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing first in torsion angle space, simulated annealing in cartesian space. Final refinement in explicit solvent (H2O).
AuthorsGronwald, W. / Maurer, T. / Fuechsl, R. / Wohlgemuth, S. / Herrmann, C. / Kalbitzer, H.R.
Citation
Journal: To be Published
Title: New insights into binding of the possible cancer target RalGDS
Authors: Gronwald, W. / Maurer, T. / Fuechsl, R. / Wohlgemuth, S. / Herrmann, C. / Kalbitzer, H.R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 1997
Title: Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling.
Authors: Geyer, M. / Herrmann, C. / Wohlgemuth, S. / Wittinghofer, A. / Kalbitzer, H.R.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 1997
Title: Three-dimensional structure of the Ras-interacting domain of RalGDS.
Authors: Huang, L. / Weng, X. / Hofer, F. / Martin, G.S. / Kim, S.H.
History
DepositionSep 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Ral guanine nucleotide dissociation stimulator


Theoretical massNumber of molelcules
Total (without water)10,0521
Polymers10,0521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ral guanine nucleotide dissociation stimulator / RalGEF / RalGDS


Mass: 10052.413 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALGDS, RGF / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12967

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1332D NOESY
NMR detailsText: sequential assignment bassed on triple resonance spectra, 2D 1H TOCSY, 3D 15N edited TOCSY, 3D 13C edited TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium buffer at ph 7.0, 2 mM dithioerythritol (DTE), 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM 2,2-dimethyl-2-silapentane sulfonic acid (DSS) 1.0 mM RalGDS-RBD non labeled95% H2O/5% D2O (v/v)
220 mM potassium buffer at ph 7.0, 2 mM dithioerythritol (DTE), 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM 2,2-dimethyl-2-silapentane sulfonic acid (DSS) 2.9 mM RalGDS-RBD 15N/13C labeled95% H2O/5% D2O (v/v)
320 mM potassium buffer at ph 7.0, 2 mM dithioerythritol (DTE), 0.5 mM EDTA, 0.5 mM NaN3, 0.1 mM 2,2-dimethyl-2-silapentane sulfonic acid (DSS) 1.0 mM RalGDS-RBD non labeled100% D2O
Sample conditionsIonic strength: 20 mM potassium buffer / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
AUREMOL2.2Gronwald, Trenner, Brunner, Ganslmeier, Neidig & Kalbitzerdata analysis
CNS1.1Br ngerstructure solution
XPLOR-NIH2.9.6Schwietersrefinement
AUREMOL2.2Gronwald, Trenner, Brunner, Ganslmeier, Neidig & Kalbitzeriterative matrix relaxation
RefinementMethod: simulated annealing first in torsion angle space, simulated annealing in cartesian space. Final refinement in explicit solvent (H2O).
Software ordinal: 1
Details: The structures are based on a total of 1680 restraints, 1550 are NOE-derived distance constraints, 104 dihedral angle restraints,26 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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