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- PDB-5cm9: Structural Basis for the Selectivity of Guanine Nucleotide Exchan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cm9 | ||||||
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Title | Structural Basis for the Selectivity of Guanine Nucleotide Exchange Factors for the small G-protein Ral | ||||||
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![]() | SIGNALING PROTEIN / Complex G-protein Exchange Factor | ||||||
Function / homology | ![]() R3/R4 cell fate commitment / regulation of Ral protein signal transduction / border follicle cell migration / RAF/MAP kinase cascade / negative regulation of JNK cascade / regulation of cell morphogenesis / Flemming body / negative regulation of cardiac muscle cell apoptotic process / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of stem cell proliferation ...R3/R4 cell fate commitment / regulation of Ral protein signal transduction / border follicle cell migration / RAF/MAP kinase cascade / negative regulation of JNK cascade / regulation of cell morphogenesis / Flemming body / negative regulation of cardiac muscle cell apoptotic process / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of stem cell proliferation / cleavage furrow / negative regulation of innate immune response / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / PDZ domain binding / receptor internalization / GDP binding / 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 | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Popovic, M. / Schouten, A. / Rehmann, H. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.8 KB | Display | ![]() |
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PDB format | ![]() | 176.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 477.6 KB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cm8C ![]() 4jgwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52113.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 23117.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.45 Details: 15% PEG 3350, 200 mM ammonium acetate, 100 mM Bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97488 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.6→2.7 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.69 / % possible all: 56.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JGW as poly Ala model 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.171 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→46.63 Å
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Refine LS restraints |
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