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- PDB-6xar: Structure of CBL tyrosine kinase binding domain (TKBD) with C-ter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xar | |||||||||
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Title | Structure of CBL tyrosine kinase binding domain (TKBD) with C-terminal tail of Src-like kinase protein 2 (SLAP2) | |||||||||
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![]() | SIGNALING PROTEIN / adaptor / E3 ubiquitin ligase / activation / complex | |||||||||
Function / homology | ![]() Negative regulation of FLT3 / negative regulation of calcium-mediated signaling / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / : / entry of bacterium into host cell / flotillin complex / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding ...Negative regulation of FLT3 / negative regulation of calcium-mediated signaling / regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / : / entry of bacterium into host cell / flotillin complex / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / phosphatidylinositol 3-kinase complex / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of T cell receptor signaling pathway / Regulation of KIT signaling / 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 / TGF-beta receptor signaling activates SMADs / response to starvation / protein monoubiquitination / phosphatidylinositol phosphate biosynthetic process / protein autoubiquitination / signaling adaptor activity / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / T cell activation / ephrin receptor binding / phosphotyrosine residue binding / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / response to activity / 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 / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / Constitutive Signaling by EGFRvIII / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / cilium / 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 / ubiquitin protein ligase activity / late endosome / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / growth cone / cellular response to hypoxia / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / response to ethanol / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / intracellular membrane-bounded organelle / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Wybenga-Groot, L.E. / McGlade, C.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: SLAP2 Adaptor Binding Disrupts c-CBL Autoinhibition to Activate Ubiquitin Ligase Function. Authors: Wybenga-Groot, L.E. / Tench, A.J. / Simpson, C.D. / Germain, J.S. / Raught, B. / Moran, M.F. / McGlade, C.J. #1: ![]() Title: Sleuthing biochemical evidence to elucidate unassigned electron density in a CBL-SLAP2 crystal complex Authors: Wybenga-Groot, L.E. / McGlade, C.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.2 KB | Display | ![]() |
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PDB format | ![]() | 107.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.5 KB | Display | ![]() |
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Full document | ![]() | 464.4 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b47S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38832.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22681, RING-type E3 ubiquitin transferase #2: Protein/peptide | Mass: 2067.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | The mouse SLAP2 construct was degraded during crystallization. The originally expressed sequence, ...The mouse SLAP2 construct was degraded during crystallization. The originally expressed sequence, after tag cleavage, was GSQPERHKVT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.9 % / Description: rod-like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: CBL/SLAP2 complex mixed in hanging drop with equal volume (200 nL) of 0.1 M Hepes pH 7.5, 10% (w/v) PEG8000 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2010 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→45.323 Å / Num. obs: 20374 / % possible obs: 90.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 40.17 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.055 / Rrim(I) all: 0.098 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B47 Resolution: 2.501→45.323 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.2 / 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: 112.68 Å2 / Biso mean: 48.5193 Å2 / Biso min: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.501→45.323 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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