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Open data
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Basic information
Entry | Database: PDB / ID: 6y44 | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated SOS1 peptide | ||||||
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![]() | PROTEIN BINDING / 14-3-3 / SOS1 / complex / protein / protein-protein interactions | ||||||
Function / homology | ![]() 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 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Regulation of KIT signaling / leukocyte migration / regulation of T cell proliferation / NRAGE signals death through JNK / roof of mouth development / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / neurotrophin TRK receptor signaling pathway / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Signalling to RAS / negative regulation of keratinocyte proliferation / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / establishment of skin barrier / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / RHO GTPases activate PKNs / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / protein kinase A signaling / GRB2 events in EGFR signaling / protein sequestering activity / SHC1 events in EGFR signaling / RAC1 GTPase cycle / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / negative regulation of innate immune response / myelination / Signaling by FGFR1 in disease / protein export from nucleus / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / GTPase activator activity / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / molecular condensate scaffold activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / stem cell proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y3mC ![]() 6y3oC ![]() 6y3rC ![]() 6y3sC ![]() 6y3vC ![]() 6y40C ![]() 6y8aC ![]() 6y8bC ![]() 6y8dC ![]() 6y8eC ![]() 3lw1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1522.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 246 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 28% (v/v) PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.541 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→29.81 Å / Num. obs: 31307 / % possible obs: 99.85 % / Redundancy: 6 % / CC1/2: 0.9 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.712→1.773 Å / Num. unique obs: 3088 / CC1/2: 0.9 / % possible all: 99.01 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LW1 Resolution: 1.71→29.81 Å / SU ML: 0.1878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0858
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→29.81 Å
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Refine LS restraints |
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LS refinement shell |
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