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Yorodumi- PDB-7ta6: Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ta6 | ||||||||||||
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Title | Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / tumor necrosis factor-alpha / signaling | ||||||||||||
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 vitamin D biosynthetic process ...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 vitamin D biosynthetic process / response to macrophage colony-stimulating factor / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / 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 / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / : / death receptor agonist activity / negative regulation of myelination / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / response to isolation stress / positive regulation of calcidiol 1-monooxygenase activity / inflammatory response to wounding / sequestering of triglyceride / positive regulation of action potential / positive regulation of I-kappaB phosphorylation / positive regulation of interleukin-18 production / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / response to fructose / cellular response to toxic substance / positive regulation of neuroinflammatory response / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of mononuclear cell migration / positive regulation of synoviocyte proliferation / leukocyte tethering or rolling / positive regulation of fever generation / negative regulation of myoblast differentiation / negative regulation of D-glucose import / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / macrophage activation involved in immune response / positive regulation of protein localization to cell surface / negative regulation of oxidative phosphorylation / TNFR1-mediated ceramide production / positive regulation of cytokine production involved in inflammatory response / negative regulation of systemic arterial blood pressure / tumor necrosis factor receptor binding / positive regulation of osteoclast differentiation / regulation of immunoglobulin production / regulation of metabolic process / positive regulation of heterotypic cell-cell adhesion / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex disassembly / positive regulation of programmed cell death / positive regulation of podosome assembly / positive regulation of hepatocyte proliferation / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / negative regulation of viral genome replication / positive regulation of DNA biosynthetic process / regulation of synapse organization / negative regulation of fat cell differentiation / : / negative regulation of endothelial cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / skeletal muscle contraction / negative regulation of apoptotic signaling pathway / phagocytic cup / humoral immune response / negative regulation of lipid storage / negative regulation of mitotic cell cycle / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway via death domain receptors Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||||||||
Authors | Niu, J. / Bingman, C.A. / Gellman, S.H. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Trimer-to-Monomer Disruption Mechanism for a Potent, Protease-Resistant Antagonist of Tumor Necrosis Factor-alpha Signaling. Authors: Niu, J. / Cederstrand, A.J. / Eddinger, G.A. / Yin, B. / Checco, J.W. / Bingman, C.A. / Outlaw, V.K. / Gellman, S.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ta6.cif.gz | 753.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ta6.ent.gz | 646.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ta6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ta6_validation.pdf.gz | 594.7 KB | Display | wwPDB validaton report |
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Full document | 7ta6_full_validation.pdf.gz | 612.3 KB | Display | |
Data in XML | 7ta6_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 7ta6_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/7ta6 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/7ta6 | HTTPS FTP |
-Related structure data
Related structure data | 7ta3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
-Components
-Protein / Protein/peptide , 2 types, 16 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 17457.736 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNF, TNFA, TNFSF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01375 #2: Protein/peptide | Mass: 3293.842 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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-Non-polymers , 4 types, 62 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-K / | #5: Chemical | ChemComp-NH2 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 8.5 Details: 0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03323 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.67→101.11 Å / Num. obs: 43735 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 75.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Net I/σ(I): 9.5 / Num. measured all: 298842 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TNF_A Resolution: 2.67→39.74 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 228.26 Å2 / Biso mean: 101.43 Å2 / Biso min: 54.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→39.74 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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