+Open data
-Basic information
Entry | Database: PDB / ID: 4nn6 | ||||||
---|---|---|---|---|---|---|---|
Title | Cytokine receptor complex - Crystal form 1B | ||||||
Components |
| ||||||
Keywords | 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 | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å | ||||||
Authors | Verstraete, K. / van Schie, L. / Savvides, S.N. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nn6.cif.gz | 257.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nn6.ent.gz | 210.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nn6_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4nn6_full_validation.pdf.gz | 466.9 KB | Display | |
Data in XML | 4nn6_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4nn6_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/4nn6 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/4nn6 | HTTPS FTP |
-Related structure data
Related structure data | 4nn5SC 4nn7C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Mus musculus (house mouse) / Gene: Tslp / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9JIE6 |
---|---|
#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.) Mus musculus (house mouse) / Gene: Il7r, IL7RA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3) / References: UniProt: P16872 |
#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.) Mus musculus (house mouse) / Gene: Crlf2, CRLF2 (TSLPR), Crlm2, Tpte2, Tslpr / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8CII9 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9686 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|