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- PDB-5hkz: Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hkz | ||||||
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Title | Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8 A Resolution (P21 form) | ||||||
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![]() | LIGASE / SPRY2 / Cbl / Protein-protein interaction / anticancer target | ||||||
Function / homology | ![]() microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway / animal organ development ...microtubule end / lung growth / negative regulation of lens fiber cell differentiation / negative regulation of cell projection organization / ubiquitin-protein transferase inhibitor activity / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / negative regulation of fibroblast growth factor receptor signaling pathway / animal organ development / negative regulation of vascular endothelial growth factor signaling pathway / regulation of Rap protein signal transduction / bud elongation involved in lung branching / entry of bacterium into host cell / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / protein serine/threonine kinase inhibitor activity / negative regulation of Ras protein signal transduction / negative regulation of epithelial to mesenchymal transition / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / inner ear morphogenesis / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of peptidyl-threonine phosphorylation / TGF-beta receptor signaling activates SMADs / response to starvation / protein monoubiquitination / establishment of mitotic spindle orientation / cellular response to vascular endothelial growth factor stimulus / fibroblast growth factor receptor signaling pathway / cell fate commitment / protein autoubiquitination / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / ERK1 and ERK2 cascade / ephrin receptor binding / phosphotyrosine residue binding / protein serine/threonine kinase activator activity / negative regulation of angiogenesis / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / cellular response to leukemia inhibitory factor / Regulation of signaling by CBL / response to gamma radiation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / sensory perception of sound / Negative regulation of FGFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / cilium / ruffle membrane / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / microtubule cytoskeleton / ubiquitin protein ligase activity / actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / protein ubiquitination / positive regulation of cell migration / cadherin binding / membrane raft / negative regulation of cell population proliferation / focal adhesion / DNA damage response / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Zhang, N. / Cooper, A. / Gao, P. / Perez, R.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8 A Resolution (P21 form) Authors: Zhang, N. / Ferris, D. / Lovell, S. / Smalter-Hall, A. / Battaile, K.P. / Anbanandam, A. / Gao, P. / Hanzlik, R. / Perez, R.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.8 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bumS 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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Unit cell |
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Components
#1: Protein | Mass: 35702.219 Da / Num. of mol.: 1 Fragment: Tyrosine kinase binding domain (TKBD), residues 47-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 2992.173 Da / Num. of mol.: 1 / Fragment: unp residues 36-60 / Source method: obtained synthetically Details: Synthesized by New England Peptide with an acetylated N-terminus Source: (synth.) ![]() |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (w/v) PEG 2000 MME, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→43.15 Å / Num. obs: 28815 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.3 / Num. measured all: 95633 / Scaling rejects: 2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BUM Resolution: 1.8→39.668 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 21.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.55 Å2 / Biso mean: 25.0576 Å2 / Biso min: 9.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→39.668 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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