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Yorodumi- PDB-3mxc: Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mxc | ||||||
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Title | Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications. | ||||||
Components |
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Keywords | PROTEIN BINDING / Protein-peptide complex / AICD / Grb2-SH2 / ALZHEIMER'S DISEASE / APP | ||||||
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 / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator 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 / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / Signaling by cytosolic FGFR1 fusion mutants / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / Interleukin-15 signaling / axon midline choice point recognition / astrocyte activation involved in immune response / MET activates PTPN11 / regulation of spontaneous synaptic transmission / MET activates RAP1 and RAC1 / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / ciliary rootlet / Signal regulatory protein family interactions / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Regulation of KIT signaling / epidermal growth factor receptor binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / STAT5 activation downstream of FLT3 ITD mutants / dendrite development / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / regulation of MAPK cascade / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / neuromuscular process controlling balance / RHOU GTPase cycle / regulation of presynapse assembly / The NLRP3 inflammasome / PI3K events in ERBB2 signaling / intracellular copper ion homeostasis / transition metal ion binding / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / regulation of multicellular organism growth / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / negative regulation of neuron differentiation / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / ECM proteoglycans / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / spindle midzone / positive regulation of T cell migration / 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 / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sen, U. / Das, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Functional Implications of the Conformational Switch in AICD Peptide upon Binding to Grb2-SH2 Domain. Authors: Das, S. / Raychaudhuri, M. / Sen, U. / Mukhopadhyay, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mxc.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mxc.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxc ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxc | HTTPS FTP |
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-Related structure data
Related structure data | 3mxyC 1jyrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11729.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Plasmid: pET(28a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62993 |
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#2: Protein/peptide | Mass: 1165.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P05067*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % |
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Crystal grow | Temperature: 293 K Details: 0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 8.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 2, 2009 / Details: OSMIC MAX-FLUX |
Radiation | Monochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 8497 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 5.48 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.0423 / Rsym value: 0.0343 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.23 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JYR Resolution: 2→29.69 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1299777.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.78 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 8
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Xplor file |
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