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Yorodumi- PDB-5hkx: Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refin... -
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-Basic information
Entry | Database: PDB / ID: 5hkx | ||||||
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Title | Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution | ||||||
Components | E3 ubiquitin-protein ligase CBL | ||||||
Keywords | LIGASE / SPRY2 / Cbl / Protein-protein interaction / anticancer target | ||||||
Function / homology | Function and homology information ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Rap protein signal transduction / entry of bacterium into host cell / negative regulation of epidermal growth factor receptor signaling pathway / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation ...ubiquitin-dependent endocytosis / regulation of platelet-derived growth factor receptor-alpha signaling pathway / regulation of Rap protein signal transduction / entry of bacterium into host cell / negative regulation of epidermal growth factor receptor signaling pathway / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to testosterone / cellular response to platelet-derived growth factor stimulus / response to starvation / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / protein autoubiquitination / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / ephrin receptor binding / phosphotyrosine residue binding / EGFR downregulation / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to nerve growth factor stimulus / Constitutive Signaling by EGFRvIII / response to activity / Regulation of signaling by CBL / response to gamma radiation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin-protein transferase activity / Cargo recognition for clathrin-mediated endocytosis / male gonad development / ubiquitin protein ligase activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / cellular response to hypoxia / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Zhang, N. / Cooper, A. / Gao, P. / Perez, R.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hkx.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hkx.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/5hkx ftp://data.pdbj.org/pub/pdb/validation_reports/hk/5hkx | HTTPS FTP |
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-Related structure data
Related structure data | 3bumS 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
#1: Protein | Mass: 45166.898 Da / Num. of mol.: 1 Fragment: Tyrosine kinase binding and RING domains (TKBD-RING), residues 47-435 Mutation: Y371E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLyseS-RARE References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% (w/v) PEG 5000 MME, 0.1M MES, 12% (v/v) 1-propanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
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: 1.85→41.24 Å / Num. obs: 35622 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.9 / Num. measured all: 120005 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BUM Resolution: 1.85→34.468 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 22.02 / 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: 80.05 Å2 / Biso mean: 28.318 Å2 / Biso min: 11.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→34.468 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: 13
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