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- PDB-3in8: Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexib... -
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Basic information
Entry | Database: PDB / ID: 3in8 | ||||||
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Title | Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic | ||||||
![]() | Growth factor receptor-bound protein 2 | ||||||
![]() | SIGNALING PROTEIN/PEPTIDE / ligand preorganization / Golgi apparatus / PEPTIDE MIMICS / Host-virus interaction / Phosphoprotein / SH2 domain / SH3 / SIGNALING PROTEIN / SIGNALING PROTEIN-pseudopeptide ligand complex / SIGNALING PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | ![]() guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / vesicle membrane / 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 / Activated NTRK2 signals through PI3K / vesicle membrane / 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 / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / 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 / 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 / Signalling to RAS / RHO GTPases Activate WASPs and WAVEs / fibroblast growth factor receptor signaling pathway / signal transduction in response to DNA damage / SHC-related events triggered by IGF1R / GAB1 signalosome / 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 / 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 / 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 / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / ephrin receptor binding / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / InlB-mediated entry of Listeria monocytogenes into host cell / 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 / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / EGFR downregulation / Negative regulation of FGFR1 signaling / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / Spry regulation of FGF signaling Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Benfield, A.P. / Clements, J.H. | ||||||
![]() | ![]() Title: Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. Authors: Delorbe, J.E. / Clements, J.H. / Teresk, M.G. / Benfield, A.P. / Plake, H.R. / Millspaugh, L.E. / Martin, S.F. #1: ![]() Title: Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions Authors: Benfield, A.P. / Teresk, M.G. / Plake, H.R. / DeLorbe, J.E. / Millspaugh, L.E. / Martin, S.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.9 KB | Display | ![]() |
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PDB format | ![]() | 25.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.4 KB | Display | ![]() |
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Full document | ![]() | 768.3 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3imdC ![]() 3imjC ![]() 3in7C ![]() 3kfjC ![]() 1jyrS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 13758.543 Da / Num. of mol.: 1 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Details: residues 53-163 were expressed in addition to a C-terminal 6-his tag Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FYI / |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.762 Å3/Da / Density % sol: 30.187 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ligand in lyophilized powder form was dissolved in a 15.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1. 3.5 uL of this solution was mixed with 3.5 uL ...Details: Ligand in lyophilized powder form was dissolved in a 15.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1. 3.5 uL of this solution was mixed with 3.5 uL of 5.0 M sodium formate, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after six weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2005 |
Radiation | Monochromator: blue max-flux confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 11547 / Num. obs: 11224 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.054 / Χ2: 1.545 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.174 / Num. unique all: 889 / Χ2: 1.423 / % possible all: 79.7 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1JYR Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 48.876 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.5 Å2 / Biso mean: 17.748 Å2 / Biso min: 7.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Xplor file |
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