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 Yorodumi
Yorodumi- PDB-7ta6: Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-... -
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- Basic information
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 bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / positive regulation of fractalkine production / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / response to 3,3',5-triiodo-L-thyronine ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / positive regulation of fractalkine production / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / response to 3,3',5-triiodo-L-thyronine / positive regulation of protein transport / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / response to macrophage colony-stimulating factor / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / response to gold nanoparticle / negative regulation of vascular wound healing / negative regulation of cytokine production involved in immune response / negative regulation of amyloid-beta clearance / positive regulation of interleukin-18 production / inflammatory response to wounding / death receptor agonist activity / positive regulation of action potential / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / negative regulation of D-glucose import / embryonic digestive tract development / leukocyte migration involved in inflammatory response / vascular endothelial growth factor production / positive regulation of fever generation / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / necroptotic signaling pathway / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of mononuclear cell migration / leukocyte tethering or rolling / positive regulation of hepatocyte proliferation / negative regulation of myoblast differentiation / positive regulation of protein-containing complex disassembly / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of oxidative phosphorylation / cellular response to toxic substance / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / negative regulation of systemic arterial blood pressure / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of programmed cell death / negative regulation of mitotic cell cycle / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of fat cell differentiation / response to L-glutamate / regulation of canonical NF-kappaB signal transduction / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / TNFR1-induced proapoptotic signaling / negative regulation of bicellular tight junction assembly / regulation of metabolic process / regulation of reactive oxygen species metabolic process / positive regulation of DNA biosynthetic process / negative regulation of heart rate / negative regulation of viral genome replication / positive regulation of amyloid-beta formation / response to isolation stress / negative regulation of fat cell differentiation / regulation of synapse organization / negative regulation of endothelial cell proliferation / positive regulation of JUN kinase activity / positive regulation of MAP kinase activity / Interleukin-10 signaling / negative regulation of interleukin-6 production / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of glial cell proliferation / negative regulation of lipid storage / extrinsic apoptotic signaling pathway via death domain receptors / cell surface receptor signaling pathway via JAK-STAT / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / skeletal muscle contraction / negative regulation of osteoblast differentiation / detection of mechanical stimulus involved in sensory perception of pain 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 visualization
| Structure viewer | Molecule:  Molmil  Jmol/JSmol | 
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- Downloads & links
Downloads & links
- Download
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 ( | 
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| Similar structure data | Similarity search - Function & homology  F&H Search | 
- Links
Links
- Assembly
Assembly
- Components
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
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
Processing
| Software | 
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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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