+Open data
-Basic information
Entry | Database: PDB / ID: 3d85 | ||||||
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Title | Crystal structure of IL-23 in complex with neutralizing FAB | ||||||
Components |
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Keywords | IMMUNE SYSTEM/CYTOKINE / Interleukin-23 / FAB / IMMUNE SYSTEM-CYTOKINE COMPLEX | ||||||
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 / Fc-gamma receptor I complex 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 / complement-dependent cytotoxicity / 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 / IgG immunoglobulin complex / 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 / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / T-helper 1 type immune response / Initial triggering of complement / 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 / FCGR activation / negative regulation of protein secretion / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / negative regulation of smooth muscle cell proliferation / cytokine activity / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of actin dynamics for phagocytic cup formation / 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 / antibacterial humoral response / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to virus / defense response to Gram-negative bacterium / adaptive immune response / receptor complex / blood microparticle / 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 exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3d85.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d85.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d85_validation.pdf.gz | 480.4 KB | Display | wwPDB validaton report |
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Full document | 3d85_full_validation.pdf.gz | 496.2 KB | Display | |
Data in XML | 3d85_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 3d85_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/3d85 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/3d85 | HTTPS FTP |
-Related structure data
Related structure data | 3d87C 1ngyS 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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Details | The biological assembly is a hetero-tetramer with chains A and B representing the FAB, chain C is IL-23 subunit p19 and chain D is IL-23 subunit p40. One hetero-tetramer is located within the asymmetric unit. |
-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 19669.137 Da / Num. of mol.: 1 / 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 |
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-Antibody , 3 types, 3 molecules ABD
#1: Antibody | Mass: 23454.979 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 23843.705 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01857*PLUS |
#4: Antibody | Mass: 34753.973 Da / Num. of mol.: 1 / 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 |
-Non-polymers , 3 types, 909 molecules
#5: Chemical | ChemComp-IMD / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 7% PEG 6000, 100mM Imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 24, 2005 |
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: 1.9→106.6 Å / Num. all: 77469 / Num. obs: 77159 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30.449 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.1 / Num. unique all: 7636 / Rsym value: 0.466 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ngy Resolution: 1.9→106.6 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: 38.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→106.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Total num. of bins used: 9
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