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Yorodumi- PDB-2zpx: TNF Receptor Subtype One-selective TNF Mutant with Antagonistic A... -
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-Basic information
Entry | Database: PDB / ID: 2zpx | ||||||
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Title | TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity; R1antTNF-T8 | ||||||
Components | Tumor necrosis factor | ||||||
Keywords | CYTOKINE / Tumor necrosis factor / Trimer / Antagonistic activity / TNFR1 specific / Phage display system / Cell membrane / Lipoprotein / Membrane / Myristate / Phosphoprotein / Polymorphism / Secreted / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / regulation of synapse organization / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / Interleukin-10 signaling / antiviral innate immune response / negative regulation of interleukin-6 production / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of insulin secretion / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of lipid storage / skeletal muscle contraction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Mukai, Y. / Nakamura, T. / Yamagata, Y. / Tsutsumi, Y. | ||||||
Citation | Journal: J.Biochem. / Year: 2009 Title: Fast binding kinetics and conserved 3D structure underlie the antagonistic activity of mutant TNF: useful information for designing artificial proteo-antagonists Authors: Mukai, Y. / Nakamura, T. / Yoshioka, Y. / Shibata, H. / Abe, Y. / Nomura, T. / Taniai, M. / Ohta, T. / Nakagawa, S. / Tsunoda, S. / Kamada, H. / Yamagata, Y. / Tsutsumi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zpx.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpx.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpx ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpx | HTTPS FTP |
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-Related structure data
Related structure data | 1tnfS 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: Protein | Mass: 17283.436 Da / Num. of mol.: 3 / Fragment: UNP residues 77-233 Mutation: K11M, K65S, A84T, V85P, S86A, Y87I, Q88N, T89R, K90P, K98R, K112N, K128P Source method: isolated from a genetically manipulated source Details: this mutant was created by phage display system / Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: TNF, TNFA, TNFSF2 / Plasmid: PYAS(MODIFIED FROM PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01375 #2: Water | ChemComp-HOH / | |
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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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG1500, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Temp details: 15% PEG1500, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU |
Detector | Detector: CCD / Date: Nov 6, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→55.67 Å / Num. obs: 10337 / % possible obs: 92.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.244 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.16 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TNF Resolution: 2.83→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1361839.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.277 Å2 / ksol: 0.15 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.83→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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