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Open data
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Basic information
Entry | Database: PDB / ID: 3duh | ||||||
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Title | Structure of Interleukin-23 | ||||||
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![]() | IMMUNE SYSTEM/CYTOKINE / four-helix bundle cytokine / Ig domain / Cytokine / Glycoprotein / Immunoglobulin domain / Secreted / Antiviral defense / Immune response / Inflammatory response / Innate immunity / Tissue remodeling / IMMUNE SYSTEM / IMMUNE SYSTEM-CYTOKINE COMPLEX | ||||||
Function / homology | ![]() late endosome lumen / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...late endosome lumen / regulation of tyrosine phosphorylation of STAT protein / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell activation / positive regulation of lymphocyte proliferation / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of tissue remodeling / positive regulation of activation of Janus kinase activity / tissue remodeling / sexual reproduction / positive regulation of T-helper 1 type immune response / positive regulation of NK T cell activation / positive regulation of smooth muscle cell apoptotic process / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / positive regulation of memory T cell differentiation / natural killer cell activation / T-helper cell differentiation / positive regulation of osteoclast differentiation / Interleukin-23 signaling / negative regulation of interleukin-17 production / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Interleukin-12 signaling / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / T-helper 1 type immune response / negative regulation of interleukin-10 production / cytokine binding / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of interleukin-10 production / positive regulation of cell adhesion / negative regulation of protein secretion / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of inflammatory response to antigenic stimulus / positive regulation of defense response to virus by host / regulation of cytokine production / positive regulation of interleukin-12 production / cytokine activity / negative regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / receptor complex / inflammatory response / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lupardus, P.J. / Garcia, K.C. | ||||||
![]() | ![]() Title: The structure of interleukin-23 reveals the molecular basis of p40 subunit sharing with interleukin-12. Authors: Lupardus, P.J. / Garcia, K.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.2 KB | Display | ![]() |
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PDB format | ![]() | 146.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483 KB | Display | ![]() |
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Full document | ![]() | 498.2 KB | Display | |
Data in XML | ![]() | 34.3 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f45S 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 35811.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 19638.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gp67 signal sequence at N-terminus and 6xHis tag at C-terminus Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350, 0.2M potassium nitrate, 0.1M Hepes-NaOH pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 4, 2008 |
Radiation | Monochromator: Si(111), Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 49424 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.5 / Num. unique all: 7208 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: human p40 from PDB ID 1F45 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.997 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.243 / 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: 46.587 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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