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- PDB-1rax: RA-DOMAIN OF RAL GUANOSINE-NUCLEOTIDE DISSOCIATION STIMULATOR -

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Basic information

Entry
Database: PDB / ID: 1rax
TitleRA-DOMAIN OF RAL GUANOSINE-NUCLEOTIDE DISSOCIATION STIMULATOR
ComponentsPROTEIN (RA-DOMAIN OF RAL GUANOSINE DISSOCIATION STIMULATOR)
KeywordsRAS-BINDING DOMAIN / RALGEF / RALGDS / RAS / RA
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
AuthorsMueller, T.D. / Handel, L. / Schmieder, P. / Oschkinat, H.
Citation
Journal: To be Published
Title: High-Resolution Structure of the Ra-Domain of Human Ralgds and a Dynamics Study of its Binding Loop to Ras
Authors: Mueller, T.D. / Handel, L. / Schmieder, P. / Oschkinat, H.
#1: Journal: Nat.Struct.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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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
DepositionMar 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 27, 2021Group: Data collection / Database references / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.5Dec 27, 2023Group: 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: PROTEIN (RA-DOMAIN OF RAL GUANOSINE DISSOCIATION STIMULATOR)


Theoretical massNumber of molelcules
Total (without water)12,8891
Polymers12,8891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20STRUCTURES WITH THE LOWEST TOTAL ENERGY AND NOE ENERGY WERE SELECTED
RepresentativeModel #1

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Components

#1: Protein PROTEIN (RA-DOMAIN OF RAL GUANOSINE DISSOCIATION STIMULATOR)


Mass: 12888.555 Da / Num. of mol.: 1 / Fragment: RAS-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALGDS / Plasmid: PGEX-2T / Gene (production host): HUMAN RALGDS GENE (RALGDS) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / 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

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
AURELIA2.1Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerstructure calculation
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST TOTAL ENERGY AND NOE ENERGY WERE SELECTED
Conformers calculated total number: 20 / Conformers submitted total number: 10

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