+Open data
-Basic information
Entry | Database: PDB / ID: 2w0z | ||||||
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Title | Grb2 SH3C (3) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / POLYMORPHISM / PHOSPHOPROTEIN / GOLGI APPARATUS / ALTERNATIVE SPLICING / HOST-VIRUS INTERACTION / SH3C / GRB2 / SIGNALING / SH2 DOMAIN / SH3 DOMAIN | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / positive regulation of mast cell degranulation / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / phosphatidylinositol-3,4-bisphosphate binding ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / positive regulation of mast cell degranulation / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / phosphatidylinositol-3,4-bisphosphate binding / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / 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 / osteoclast differentiation / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Harkiolaki, M. / Tsirka, T. / Feller, S.M. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Distinct Binding Modes of Two Epitopes in Gab2 that Interact with the Sh3C Domain of Grb2. Authors: Harkiolaki, M. / Tsirka, T. / Lewitzky, M. / Simister, P.C. / Joshi, D. / Bird, L.E. / Jones, E.Y. / O'Reilly, N. / Feller, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0z.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0z.ent.gz | 17.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0z ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0z | HTTPS FTP |
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-Related structure data
Related structure data | 2vvkC 2vwfC 2w10C 2vdfS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 6612.233 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 159-214 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-TERMINAL GP- OVERHANG DUE TO INFUSION VECTOR USED Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: OPIN J / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62993 | ||
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#2: Protein/peptide | Mass: 958.155 Da / Num. of mol.: 1 / Fragment: SH3 BINDING REGION, RESIDUES 350-358 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9UQC2 | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | N-TERMINAL GP OVERHANG DUE TO EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 32.7 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.7 M TRISODIUM CITRATE, 0.1 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 7072 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.7→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.3 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VDF Resolution: 1.7→45.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.294 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→45.13 Å
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