+Open data
-Basic information
Entry | Database: PDB / ID: 2vvk | ||||||
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Title | Grb2 SH3C (1) | ||||||
Components | GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2GRB2 | ||||||
Keywords | PROTEIN BINDING / GRB2 SH3 / SH3 DOMAIN / SH2 DOMAIN / PHOSPHOPROTEIN / HOST-VIRUS INTERACTION / PROTEIN-BINDING / GOLGI APPARATUS / ALTERNATIVE SPLICING | ||||||
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 / neurotrophin TRKA receptor binding / vesicle membrane / 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 / neurotrophin TRKA receptor binding / vesicle membrane / 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 / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / positive regulation of actin filament polymerization / endodermal cell differentiation / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / 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 / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Schwann cell development / 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 / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / myelination / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / 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 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / 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 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 2vvk.cif.gz | 26.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvk.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvk ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvk | HTTPS FTP |
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-Related structure data
Related structure data | 2vwfC 2w0zC 2w10C 1io6S 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
#1: Protein | Mass: 6363.956 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 161-214 Source method: isolated from a genetically manipulated source Details: N TERMINAL GS OVERHAND DUE TO THROMBIN CLEAVAGE / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62993 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | GS TERMINAL OVERHANG (THROMBIN CLEAVAGE) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.5 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 8% PEG 4K, 0.1M NAACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2007 / 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: 1.6→30 Å / Num. obs: 6917 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 13.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 89.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 14.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IO6 Resolution: 1.6→30.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.214 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 8.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30.79 Å
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