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- PDB-1ef5: SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF RGL -

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Basic information

Entry
Database: PDB / ID: 1ef5
TitleSOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF RGL
ComponentsRGL
KeywordsSIGNALING PROTEIN / RAS-BINDING DOMAIN / RGL / RAS / RBD / RA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


RAF/MAP kinase cascade / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity
Similarity search - Function
Ral guanine nucleotide dissociation stimulator-like 1 / 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-like 1 / 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-like 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsKigawa, T. / Endo, M. / Ito, Y. / Shirouzu, M. / Kikuchi, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: FEBS Lett. / Year: 1998
Title: Solution structure of the Ras-binding domain of RGL.
Authors: Kigawa, T. / Endo, M. / Ito, Y. / Shirouzu, M. / Kikuchi, A. / Yokoyama, S.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RGL


Theoretical massNumber of molelcules
Total (without water)11,7371
Polymers11,7371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein RGL


Mass: 11737.146 Da / Num. of mol.: 1 / Fragment: RAS-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q60695

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.5mM RGL-RBD U-15N,13C; 50mM Tris-HCl; 5mM DTT; 10mM MgCl2; 200mM NaCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200mM / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRBruker, AG.collection
XwinNMR1.3Bruker, AG.collection
Azara1Boucherprocessing
Felix95MSI, Inc.data analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1309 restraints, 1211 are NOE-derived distance constraints, 56 dihedral angle restraints, 42 distance restraints from hydrogen bonds. N-terminal ...Details: the structures are based on a total of 1309 restraints, 1211 are NOE-derived distance constraints, 56 dihedral angle restraints, 42 distance restraints from hydrogen bonds. N-terminal residues 632-646 are not defined by NMR restraints and excluded from the coordinate file.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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