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Yorodumi- PDB-6eie: Ras guanine nucleotide exchange factor SOS2 (Rem-cdc25), with sur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eie | ||||||
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Title | Ras guanine nucleotide exchange factor SOS2 (Rem-cdc25), with surface mutations | ||||||
Components | Son of sevenless homolog 2 | ||||||
Keywords | SIGNALING PROTEIN / Guanine exchange factor / GEF / SOS2 | ||||||
Function / homology | Function and homology information regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / G alpha (12/13) signalling events / insulin receptor signaling pathway / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Hillig, R.C. / Moosmayer, D. / Mastouri, J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Discovery of potent SOS1 inhibitors that block RAS activation via disruption of the RAS-SOS1 interaction. Authors: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / ...Authors: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / Siemeister, G. / Kahmann, J.D. / Wegener, D. / Bohnke, N. / Eis, K. / Graham, K. / Wortmann, L. / von Nussbaum, F. / Bader, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eie.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eie.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 6eie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/6eie ftp://data.pdbj.org/pub/pdb/validation_reports/ei/6eie | HTTPS FTP |
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-Related structure data
Related structure data | 5ovdC 5oveC 5ovfC 5ovgC 5ovhC 5oviC 6eplC 6epmC 6epnC 6epoC 6eppC 1nvuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57370.676 Da / Num. of mol.: 1 Mutation: P564Q, E707Y, Q768H, F769I, K947T, K949R, K949H, C1019P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07890 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein 10.3 mg/ml in 25 mM Tris HCl, pH 7.5, 100 mM NaCl, 1 mM DTT. Reservoir 0,1 M Natriumacetat, 20% w/v PEG 3350. Cryo buffer was reservoir supplemented with 15% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→46.54 Å / Num. obs: 13644 / % possible obs: 96.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 69.7 Å2 / CC1/2: 0.998 / Rsym value: 0.067 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.72→2.88 Å / Redundancy: 3.2 % / Num. unique obs: 1867 / CC1/2: 0.761 / Rsym value: 0.539 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NVU Resolution: 2.72→46.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 51.288 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.654 Å2
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Refinement step | Cycle: 1 / Resolution: 2.72→46.54 Å
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Refine LS restraints |
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