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- PDB-5cm9: Structural Basis for the Selectivity of Guanine Nucleotide Exchan... -

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Basic information

Entry
Database: PDB / ID: 5cm9
TitleStructural Basis for the Selectivity of Guanine Nucleotide Exchange Factors for the small G-protein Ral
Components
  • Ral guanine nucleotide dissociation stimulator-like 2
  • Ras-related protein Ral-a
KeywordsSIGNALING PROTEIN / Complex G-protein Exchange Factor
Function / homology
Function and homology information


R3/R4 cell fate commitment / regulation of Ral protein signal transduction / border follicle cell migration / RAF/MAP kinase cascade / Flemming body / regulation of cell morphogenesis / negative regulation of JNK cascade / negative regulation of cardiac muscle cell apoptotic process / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction ...R3/R4 cell fate commitment / regulation of Ral protein signal transduction / border follicle cell migration / RAF/MAP kinase cascade / Flemming body / regulation of cell morphogenesis / negative regulation of JNK cascade / negative regulation of cardiac muscle cell apoptotic process / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction / positive regulation of stem cell proliferation / cleavage furrow / negative regulation of innate immune response / guanyl-nucleotide exchange factor activity / small monomeric GTPase / PDZ domain binding / receptor internalization / GDP binding / G protein activity / defense response to Gram-negative bacterium / Ras protein signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / innate immune response / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / 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 ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / 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 / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Ral-a / Ral guanine nucleotide dissociation stimulator-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPopovic, M. / Schouten, A. / Rehmann, H.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The structure of the Guanine Nucleotide Exchange Factor Rlf in complex with the small G-protein Ral identifies conformational intermediates of the exchange reaction and the basis for the selectivity.
Authors: Popovic, M. / Schouten, A. / Rensen-de Leeuw, M. / Rehmann, H.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ral guanine nucleotide dissociation stimulator-like 2
B: Ral guanine nucleotide dissociation stimulator-like 2
C: Ras-related protein Ral-a
D: Ras-related protein Ral-a


Theoretical massNumber of molelcules
Total (without water)150,4624
Polymers150,4624
Non-polymers00
Water64936
1
A: Ral guanine nucleotide dissociation stimulator-like 2
C: Ras-related protein Ral-a


Theoretical massNumber of molelcules
Total (without water)75,2312
Polymers75,2312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-7 kcal/mol
Surface area26210 Å2
MethodPISA
2
B: Ral guanine nucleotide dissociation stimulator-like 2
D: Ras-related protein Ral-a


Theoretical massNumber of molelcules
Total (without water)75,2312
Polymers75,2312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-7 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.877, 99.828, 111.487
Angle α, β, γ (deg.)90.00, 127.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ral guanine nucleotide dissociation stimulator-like 2 / RalGDS-like 2 / RalGDS-like factor / Ras-associated protein RAB2L


Mass: 52113.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rgl2, Rab2l, Rlf / Plasmid: pGEX6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): CK600 / References: UniProt: Q61193
#2: Protein Ras-related protein Ral-a


Mass: 23117.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rala, CG2849 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): CK600 / References: UniProt: P48555
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.45
Details: 15% PEG 3350, 200 mM ammonium acetate, 100 mM Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97488 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97488 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 40751 / % possible obs: 88.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 12.72
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.69 / % possible all: 56.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JGW as poly Ala model

4jgw


Resolution: 2.6→46.63 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.867 / SU B: 15.8 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R: 1.031 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31988 2038 5 %RANDOM
Rwork0.27332 ---
obs0.27573 38712 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.171 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0.46 Å2
2--1.03 Å20 Å2
3----2.21 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8583 0 0 36 8619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.97211851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37351083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8222.847404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.876151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6341592
X-RAY DIFFRACTIONr_chiral_restr0.060.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3271.55460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63428779
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72633286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2564.53072
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 96 -
Rwork0.34 1829 -
obs--100 %

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