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Open data
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Basic information
Entry | Database: PDB / ID: 4nn6 | ||||||
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Title | Cytokine receptor complex - Crystal form 1B | ||||||
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![]() | CYTOKINE/CYTOKINE RECEPTOR / four helical bundle fold / CHR domains / TSLP cytokine signaling / TSLPR and IL-7Ralpha receptors / cell surface / CYTOKINE-CYTOKINE RECEPTOR complex | ||||||
Function / homology | ![]() interleukin-7 receptor binding / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / negative regulation of T cell apoptotic process ...interleukin-7 receptor binding / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis / positive regulation of interleukin-10 production / B cell homeostasis / hemopoiesis / T cell differentiation / lymph node development / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of interleukin-6 production / gene expression / T cell differentiation in thymus / defense response to Gram-positive bacterium / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Verstraete, K. / van Schie, L. / Savvides, S.N. | ||||||
![]() | ![]() Title: Structural basis of the proinflammatory signaling complex mediated by TSLP. Authors: Verstraete, K. / van Schie, L. / Vyncke, L. / Bloch, Y. / Tavernier, J. / Pauwels, E. / Peelman, F. / Savvides, S.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.5 KB | Display | ![]() |
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PDB format | ![]() | 210.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.6 KB | Display | ![]() |
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Full document | ![]() | 466.9 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nn5SC ![]() 4nn7C S: Starting model for refinement C: citing same article ( |
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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: 15109.947 Da / Num. of mol.: 1 / Fragment: UNP residues 20-140 / Mutation: N123Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 25431.809 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 21-239) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 22812.354 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 20-222) / Mutation: N122Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, soaked in 18% PEG4000, 0.1 M Tris-HCl, pH 7.5, 0.3 M calcium acetate for 1 hour prior to cryoprotection, VAPOR DIFFUSION, ...Details: 14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, soaked in 18% PEG4000, 0.1 M Tris-HCl, pH 7.5, 0.3 M calcium acetate for 1 hour prior to cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.545→50 Å / Num. all: 19531 / Num. obs: 19440 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.545→2.7 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.87 / Num. unique all: 3031 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NN5 Resolution: 2.545→42.449 Å / SU ML: 0.39 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: FREE R / σ(F): 2.01 / Phase error: 32.55 / 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 mean: 87.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.545→42.449 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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