+Open data
-Basic information
Entry | Database: PDB / ID: 8bea | |||||||||
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Title | Crystal structure of SOS1-HRas-peptidomimetic10 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / Stabilizer | |||||||||
Function / homology | Function and homology information midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of miRNA metabolic process / T-helper 1 type immune response / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of wound healing / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / defense response to protozoan / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / adipose tissue development / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / molecular condensate scaffold activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | |||||||||
Authors | Fischer, B. / Wohlkonig, A. / Steyaert, J. | |||||||||
Funding support | Belgium, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Nanobody Loop Mimetics Enhance Son of Sevenless 1-Catalyzed Nucleotide Exchange on RAS. Authors: Van Holsbeeck, K. / Fischer, B. / Gonzalez, S. / Gadais, C. / Versees, W. / Martins, J.C. / Martin, C. / Wohlkonig, A. / Steyaert, J. / Ballet, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bea.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bea.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8bea ftp://data.pdbj.org/pub/pdb/validation_reports/be/8bea | HTTPS FTP |
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-Related structure data
Related structure data | 8be6C 8be7C 8be8C 8be9C 1bkdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21046.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112, small monomeric GTPase |
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#2: Protein | Mass: 59348.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07889 |
#3: Protein/peptide | Mass: 1096.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium formate 3 M, Tris 100mM pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980105 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→48.66 Å / Num. obs: 41859 / % possible obs: 99.7 % / Redundancy: 27 % / Biso Wilson estimate: 42.55 Å2 / CC1/2: 0.99 / Net I/σ(I): 20.93 |
Reflection shell | Resolution: 2.47→2.62 Å / Num. unique obs: 6546 / CC1/2: 0.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BKD Resolution: 2.47→48.66 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.0509 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→48.66 Å
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Refine LS restraints |
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LS refinement shell |
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