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Open data
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Basic information
Entry | Database: PDB / ID: 5uwc | |||||||||
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Title | Cytokine-receptor complex | |||||||||
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![]() | SIGNALING PROTEIN / Cytokine / Receptor / Signalling | |||||||||
Function / homology | ![]() interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / embryonic hemopoiesis / cytokine receptor activity / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein ...interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / embryonic hemopoiesis / cytokine receptor activity / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / nervous system development / RAF/MAP kinase cascade / receptor complex / immune response / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Broughton, S.E. / Parker, M.W. | |||||||||
![]() | ![]() Title: A dual role for the N-terminal domain of the IL-3 receptor in cell signalling. Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / ...Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / Schieber, C. / Hughes, T.P. / Lopez, A.F. / Parker, M.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.3 KB | Display | ![]() |
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PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uv8C ![]() 1jliS ![]() 4jzjS 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules GI
#1: Protein | Mass: 33253.570 Da / Num. of mol.: 1 / Fragment: UNP residues 20-307 / Mutation: N212Q, A298V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13969.933 Da / Num. of mol.: 1 / Fragment: UNP residues 31-152 / Mutation: W32Y, K116W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 68 molecules ![](data/chem/img/CIT.gif)
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#5: Chemical | #6: Chemical | ChemComp-IMD / | #7: Chemical | ChemComp-EDT / {[-( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.06 % / Description: Tetragonal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 20% PEG 8000, 200 mM NaCl and 100 mM citrate-phosphate buffer pH 4.8 PH range: 4.6-5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→92.2 Å / Num. obs: 23081 / % possible obs: 99 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.39→2.4 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JZJ, 1JLI Resolution: 2.4→92.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.867 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.84 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→92.2 Å
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Refine LS restraints |
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