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Yorodumi- PDB-3l9j: Selection of a novel highly specific TNFalpha antagonist: Insight... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l9j | ||||||
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Title | Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal structure of the antagonist-TNFalpha complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TNF-alpha / antagonist / in vitro selection / Cell membrane / Cytokine / Disulfide bond / Glycoprotein / Lipoprotein / Secreted / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information kringle domain binding / platelet dense granule lumen / granular component / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation ...kringle domain binding / platelet dense granule lumen / granular component / negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of translational initiation by iron / : / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / response to gold nanoparticle / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / positive regulation of plasminogen activation / negative regulation of myelination / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / death receptor agonist activity / cellular response to toxic substance / inflammatory response to wounding / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / TNF signaling / sequestering of triglyceride / positive regulation of action potential / positive regulation of protein transport / positive regulation of interleukin-18 production / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / leukocyte migration involved in inflammatory response / embryonic digestive tract development / positive regulation of superoxide dismutase activity / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / response to fructose / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / positive regulation of protein localization to cell surface / TNFR1-mediated ceramide production / macrophage activation involved in immune response / negative regulation of glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of oxidative phosphorylation / negative regulation of systemic arterial blood pressure / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of protein-containing complex disassembly / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of programmed cell death / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / positive regulation of heterotypic cell-cell adhesion / regulation of fat cell differentiation / response to L-glutamate / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of heart rate / cortical actin cytoskeleton organization / negative regulation of fat cell differentiation / phagocytic cup / positive regulation of DNA biosynthetic process / cellular response to organic substance / regulation of synapse organization / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of endothelial cell proliferation / bone mineralization / negative regulation of blood vessel endothelial cell migration / Interleukin-10 signaling / antiviral innate immune response / negative regulation of interleukin-6 production Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Byla, P. / Andersen, M.H. / Thogersen, H.C. / Gad, H.H. / Hartmann, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Selection of a novel and highly specific TNF{alpha} antagonist: insight from the crystal structure of the antagonist-TNF{alpha} complex Authors: Byla, P. / Andersen, M.H. / Holtet, T.L. / Jacobsen, H. / Munch, M. / Gad, H.H. / Thogersen, H.C. / Hartmann, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l9j.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l9j.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 3l9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/3l9j ftp://data.pdbj.org/pub/pdb/validation_reports/l9/3l9j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15314.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7CIIH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P05452*PLUS |
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#2: Protein | Mass: 16497.684 Da / Num. of mol.: 1 / Fragment: UNP residues 85-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7CIIH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P01375 |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Sequence details | THE NUMBER 52 IS SIMPLY SKIPPED IN CHAIN C. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 0.35M MgAc, 20% 2-propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→74 Å / Num. all: 17880 / Num. obs: 17855 / % possible obs: 99.86 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TNF for chain T and 1TN3 for chain C; For 1TN3 the randomized loops was removed from teh search model. These loop is 116-122 (loop 1) and 145-150 (loop 4) Resolution: 2.1→41.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.821 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.172 / 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 max: 73.34 Å2 / Biso mean: 29.367 Å2 / Biso min: 12.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→41.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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