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- PDB-1rlf: STRUCTURE DETERMINATION OF THE RAS-BINDING DOMAIN OF THE RAL-SPEC... -

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Entry
Database: PDB / ID: 1rlf
TitleSTRUCTURE DETERMINATION OF THE RAS-BINDING DOMAIN OF THE RAL-SPECIFIC GUANINE NUCLEOTIDE EXCHANGE FACTOR RLF, NMR, 10 STRUCTURES
ComponentsRLF
KeywordsSIGNAL TRANSDUCTION PROTEIN
Function / homology
Function and homology information


regulation of Ral protein signal transduction / RAF/MAP kinase cascade / negative regulation of cardiac muscle cell apoptotic process / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor ...Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsEsser, D. / Bauer, B. / Wolthuis, R.M.F. / Wittinghofer, A. / Cool, R.H. / Bay, P.
Citation
Journal: Biochemistry / Year: 1998
Title: Structure determination of the Ras-binding domain of the Ral-specific guanine nucleotide exchange factor Rlf.
Authors: Esser, D. / Bauer, B. / Wolthuis, R.M. / Wittinghofer, A. / Cool, R.H. / Bayer, P.
#1: Journal: Embo J. / Year: 1997
Title: Stimulation of Gene Induction and Cell Growth by the Ras Effector Rlf
Authors: Wolthuis, R.M. / De Ruiter, N.D. / Cool, R.H. / Bos, J.L.
#2: Journal: Oncogene / Year: 1996
Title: Ralgds-Like Factor (Rlf) is a Novel Ras and RAP 1A-Associating Protein
Authors: Wolthuis, R.M. / Bauer, B. / Van'T Veer, L.J. / De Vries-Smits, A.M. / Cool, R.H. / Spaargaren, M. / Wittinghofer, A. / Burgering, B.M. / Bos, J.L.
History
DepositionJul 9, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: RLF


Theoretical massNumber of molelcules
Total (without water)10,0481
Polymers10,0481
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 / 30ENERGY
RepresentativeModel #1

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Components

#1: Protein RLF / RLF-RBD


Mass: 10048.376 Da / Num. of mol.: 1 / Fragment: RAS BINDING DOMAIN, RESIDUES 646 - 735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61193

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOECLEAN-TOCSY
131GS-15N-HSQC
14115N-NOESY-HMQC
15115N-TOCSY-HMQCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TWO- AND THREE-DIMENSIONAL NMR SPECTROSCOPY ON UNLABELED AND 15N LABELED RLF-RBD

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
X-PLOR3.851structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: TOTAL NUMBER OF NOE CONSTRAINTS 2287; INTRARESIDUE NOE CONSTRAINTS 804; SEQUENTIAL INTERRESIDUE CONSTRAINTS (|I-J|=1) 469; INTERRESIDUE CONSTRAINTS (1<|I-J|<5) 296; INTERRESIDUE CONSTRAINTS (|I-J|>=5) 718; BACKBONE RMSD FROM TARGET DISTANCES (ASP4-ARG90) 0.2A (COMPARED TO AVERAGE STRUCTURE) COORDINATE RMSD FROM THE AVERAGE FOR ALL HEAVY ATOM0.6A; NUMBER OF STRUCTURES USED IN ABOVE STATISTICS 10S
NMR ensembleConformer selection criteria: ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 10

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