+Open data
-Basic information
Entry | Database: PDB / ID: 5uwc | |||||||||
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Title | Cytokine-receptor complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Cytokine / Receptor / Signalling | |||||||||
Function / homology | Function and homology information interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / 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 / cytokine receptor activity / embryonic hemopoiesis / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Broughton, S.E. / Parker, M.W. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uwc.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uwc.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 5uwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uwc_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5uwc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5uwc_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5uwc_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwc ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwc | HTTPS FTP |
-Related structure data
Related structure data | 5uv8C 1jliS 4jzjS 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
-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.) Homo sapiens (human) / Gene: IL3RA, IL3R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26951 |
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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.) Homo sapiens (human) / Gene: IL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08700 |
-Sugars , 2 types, 2 molecules
#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
#5: Chemical | #6: Chemical | ChemComp-IMD / | #7: Chemical | ChemComp-EDT / {[-( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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