+Open data
-Basic information
Entry | Database: PDB / ID: 6sdf | ||||||
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Title | N-terminal SH3 domain of Grb2 protein | ||||||
Components | Growth factor receptor-bound protein 2GRB2 | ||||||
Keywords | SIGNALING PROTEIN / growth factor / Grb2 / SH3-domain | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / MET activates RAP1 and RAC1 / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / regulation of MAPK cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / 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 / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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 / signal transduction in response to DNA damage / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / 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 / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / InlB-mediated entry of Listeria monocytogenes into host cell / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to ionizing radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bolgov, A.A. / Korban, S.A. / Luzik, D.A. / Rogacheva, O.N. / Zhemkov, V.A. / Kim, M. / Skrynnikov, N.R. / Bezprozvanny, I.B. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Crystal structure of the SH3 domain of growth factor receptor-bound protein 2. Authors: Bolgov, A. / Korban, S. / Luzik, D. / Zhemkov, V. / Kim, M. / Rogacheva, O. / Bezprozvanny, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sdf.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sdf.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 6sdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/6sdf ftp://data.pdbj.org/pub/pdb/validation_reports/sd/6sdf | HTTPS FTP |
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-Related structure data
Related structure data | 1griS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6943.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Electron density is lacking for B58-B61 residues (C-terminal disordered region) Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P62993 #2: Chemical | ChemComp-MPD / ( #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.46 Å3/Da / Density % sol: 64.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, 55% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream 800 (Oxford Cryosystems) / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA Details: XtaLAB SuperNova (Rigaku Oxford Diffraction) with microfocused sealed tube Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: May 27, 2019 Details: RIGAKU HyPix-3000 - High-resolution/high-speed 2D photon counting X-ray detector |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.865 Å / Num. obs: 6312 / % possible obs: 99.92 % / Redundancy: 1.892 % / Biso Wilson estimate: 17.82 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Χ2: 1.05 / Net I/σ(I): 8.86 |
Reflection shell | Resolution: 2.5→2.5879 Å / Redundancy: 1.919 % / Rmerge(I) obs: 0.03 / Num. unique obs: 607 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GRI Resolution: 2.5→28.212 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 27.199 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 92.8 Å2 / Biso mean: 20.2 Å2 / Biso min: 0.24 Å2
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Refinement step | Cycle: final / Resolution: 2.5→28.212 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.5893 Å
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