+Open data
-Basic information
Entry | Database: PDB / ID: 6y44 | ||||||
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Title | 14-3-3 Sigma in complex with phosphorylated SOS1 peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / 14-3-3 / SOS1 / complex / protein / protein-protein interactions | ||||||
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 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / regulation of epidermal cell division / roof of mouth development / 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 / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / 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 / establishment of skin barrier / SHC-related events triggered by IGF1R / 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 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / FRS-mediated FGFR3 signaling / RHO GTPases activate PKNs / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / RAC1 GTPase cycle / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / protein export from nucleus / negative regulation of innate immune response / NCAM signaling for neurite out-growth / GTPase activator activity / SHC1 events in ERBB2 signaling / molecular condensate scaffold activity / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / guanyl-nucleotide exchange factor activity / protein sequestering activity / insulin-like growth factor receptor signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / stem cell proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y44.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y44.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y44 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y44 | HTTPS FTP |
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-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 (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 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.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 1522.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07889 |
-Non-polymers , 4 types, 246 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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