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Yorodumi- PDB-5mj4: INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mj4 | ||||||||||||
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Title | INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / SINGLE-CHAIN ANTIPARALLEL TRIPLE-HELIX COILED-COIL / IMMUNOGLOBULIN-LIKE / 4-ALPHA HELICAL BUNDLE / ANTAGONIST / N-LINKED GLYCOSYLATION / CYTOKINE-ANTAGONIST COMPLEX | ||||||||||||
Function / homology | Function and homology information late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / regulation of tyrosine phosphorylation of STAT protein / natural killer cell activation involved in immune response / 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 ...late endosome lumen / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / regulation of tyrosine phosphorylation of STAT protein / natural killer cell activation involved in immune response / 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 lymphocyte proliferation / positive regulation of activation of Janus kinase activity / tissue remodeling / sexual reproduction / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / positive regulation of NK T cell activation / 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 / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / Interleukin-23 signaling / 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 / positive regulation of granulocyte macrophage colony-stimulating factor production / Interleukin-12 signaling / response to UV-B / cytokine receptor activity / positive regulation of natural killer cell activation / 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 natural killer cell proliferation / positive regulation of interleukin-10 production / negative regulation of protein secretion / positive regulation of cell adhesion / positive regulation of T-helper 17 cell lineage commitment / T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / regulation of cytokine production / negative regulation of inflammatory response to antigenic stimulus / positive regulation of defense response to virus by host / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / negative regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / cell migration / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / defense response to virus / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / 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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||||||||
Authors | Desmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. ...Desmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. / Somers, K. / Henderikx, P. / Lasters, I. / Savvides, S. | ||||||||||||
Citation | Journal: Nature Communications / Year: 2014 Title: STRUCTURAL BASIS OF IL-23 ANTAGONISM BY AN ALPHABODY PROTEIN Authors: Desmet, J. / Verstraete, K. / Bloch, Y. / Lorent, E. / Wen, Y. / Devreese, B. / Vandenbroucke, K. / Loverix, S. / Hettmann, T. / Deroo, S. / Somers, K. / Henderikx, P. / Lasters, I. / Savvides, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mj4.cif.gz | 313.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mj4.ent.gz | 258.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mj4 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mj4 | HTTPS FTP |
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-Related structure data
Related structure data | 5mj3C 4oe8 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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-Components
#1: Antibody | Mass: 34739.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P29460 |
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#2: Protein | Mass: 19812.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9NPF7 |
#3: Protein | Mass: 11888.536 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PET16B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): PLYSS |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.2M POTASSIUM FORMATE, 20.75% W/V PEG 3350, PH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→57 Å / Num. obs: 9551 / % possible obs: 99.85 % / Redundancy: 22.29 % / Rrim(I) all: 0.116 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 23.4 % / Mean I/σ(I) obs: 5.2 / Rrim(I) all: 0.921 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OE8 4oe8 Resolution: 3.4→57 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→57 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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