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- PDB-2rgf: RBD OF RAL GUANOSINE-NUCLEOTIDE EXCHANGE FACTOR (PROTEIN), NMR, 1... -

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Basic information

Entry
Database: PDB / ID: 2rgf
TitleRBD OF RAL GUANOSINE-NUCLEOTIDE EXCHANGE FACTOR (PROTEIN), NMR, 10 STRUCTURES
ComponentsRALGEF-RBD
KeywordsRAS-BINDING DOMAIN / RALGEF / RALGDS / RAS / RBD
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 / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsGeyer, M. / Herrmann, C. / Wittinghofer, A. / Kalbitzer, H.R.
Citation
Journal: Nat.Struct.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.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Differential Interaction of the Ras Family GTP-Binding Proteins H-Ras, RAP1A, and R-Ras with the Putative Effector Molecules Raf Kinase and Ral-Guanine Nucleotide Exchange Factor
Authors: Herrmann, C. / Horn, G. / Spaargaren, M. / Wittinghofer, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Identification of the Guanine Nucleotide Dissociation Stimulator for Ral as a Putative Effector Molecule of R-Ras, H-Ras, K-Ras, and RAP
Authors: Spaargaren, M. / Bischoff, J.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Activated Ras Interacts with the Ral Guanine Nucleotide Dissociation Stimulator
Authors: Hofer, F. / Fields, S. / Schneider, C. / Martin, G.S.
#4: Journal: Embo J. / Year: 1993
Title: Characterization of a Guanine Nucleotide Dissociation Stimulator for a Ras-Related Gtpase
Authors: Albright, C.F. / Giddings, B.W. / Liu, J. / Vito, M. / Weinberg, R.A.
History
DepositionFeb 13, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RALGEF-RBD


Theoretical massNumber of molelcules
Total (without water)11,1371
Polymers11,1371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
Representative

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Components

#1: Protein RALGEF-RBD


Mass: 11136.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN RALGEF GENE (RALGDS) / Plasmid: PGEX-4T3 / Species (production host): Escherichia coli / Gene (production host): HUMAN RALGEF GENE (RALGDS) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12967

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H
12113C
13115N HETERONUCLEAR EXPERIMENTS

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX8002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
AURELIA2Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerstructure calculation
X-PLOR3.851BRUNGERstructure calculation
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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