+Open data
-Basic information
Entry | Database: PDB / ID: 3d87 | ||||||
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Title | Crystal structure of Interleukin-23 | ||||||
Components |
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Keywords | CYTOKINE / Interleukin-23 / FAB | ||||||
Function / homology | Function and homology information 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 / : / tissue remodeling / positive regulation of T-helper 1 type immune response / sexual reproduction / 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 / Interleukin-23 signaling / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / positive regulation of T-helper 17 cell lineage commitment / positive regulation of neutrophil chemotaxis / Interleukin-12 signaling / response to UV-B / cytokine receptor activity / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / T-helper 1 type immune response / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / Interleukin-10 signaling / cytokine binding / positive regulation of interleukin-10 production / positive regulation of cell adhesion / negative regulation of protein secretion / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / negative regulation of inflammatory response to antigenic stimulus / regulation of cytokine production / positive regulation of interleukin-12 production / negative regulation of smooth muscle cell proliferation / cytokine activity / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to type II interferon / cytokine-mediated signaling pathway / positive regulation of inflammatory response / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell migration / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to virus / defense response to Gram-negative bacterium / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Beyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H. / Madison, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody Authors: Beyer, B.M. / Ingram, R. / Ramanathan, L. / Reichert, P. / Le, H.V. / Madison, V. / Orth, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d87.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d87.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d87_validation.pdf.gz | 497.3 KB | Display | wwPDB validaton report |
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Full document | 3d87_full_validation.pdf.gz | 594 KB | Display | |
Data in XML | 3d87_validation.xml.gz | 45.5 KB | Display | |
Data in CIF | 3d87_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d87 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d87 | HTTPS FTP |
-Related structure data
Related structure data | 3d85SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19669.137 Da / Num. of mol.: 2 / Fragment: subunit p19 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 Plasmid details: accordining to Invitrogen Bac-to-Bac manual Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NPF7 #2: Antibody | Mass: 34753.973 Da / Num. of mol.: 2 / Fragment: subunit p40 / Mutation: N200Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 Plasmid details: accordining to Invitrogen Bac-to-Bac manual Plasmid: pFastBac Dual / Cell line (production host): Hi-Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29460 #3: Chemical | #4: Chemical | #5: Sugar | ChemComp-MAN / | |
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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: 4.31 Å3/Da / Density % sol: 71.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.26M K2HPO4, 0.5M NaH2PO4, 100 mM Imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2006 |
Radiation | Monochromator: cryogenically-cooled Si(111) double-crystal system Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20.39 Å / Num. all: 44577 / Num. obs: 41680 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 77.341 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.112 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3980 / Rsym value: 0.675 / % possible all: 10 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3d85 Resolution: 2.9→20.39 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 72.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.17 Å / Total num. of bins used: 4
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