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- PDB-7kpb: Human TNF-alpha TNFR1 complex bound to conformationally selective... -
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Basic information
Entry | Database: PDB / ID: 7kpb | ||||||
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Title | Human TNF-alpha TNFR1 complex bound to conformationally selective antibody | ||||||
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![]() | CYTOKINE/Immune System / Tumour necrosis factor alpha / TNF / asymmetric / protein-protein inhibitor / CYTOKINE / Fragment antibody / Fab / CYTOKINE-Immune System complex | ||||||
Function / homology | ![]() positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / 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 / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / 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 / 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 / positive regulation of fractalkine production / : / positive regulation of vitamin D biosynthetic process / aortic valve development / response to macrophage colony-stimulating factor / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / positive regulation of leukocyte adhesion to arterial endothelial cell / negative regulation of extracellular matrix constituent secretion / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / positive regulation of apoptotic process involved in morphogenesis / 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 / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / TNFs bind their physiological receptors / response to isolation stress / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / negative regulation of cardiac muscle hypertrophy / tumor necrosis factor binding / negative regulation of amyloid-beta clearance / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / sequestering of triglyceride / positive regulation of interleukin-18 production / positive regulation of action potential / TNF signaling / positive regulation of protein transport / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of neuroinflammatory response / leukocyte tethering or rolling / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / positive regulation of mononuclear cell migration / negative regulation of myoblast differentiation / negative regulation of 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 / TNFR1-mediated ceramide production / negative regulation of oxidative phosphorylation / positive regulation of osteoclast differentiation / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cytokine production involved in inflammatory response / tumor necrosis factor receptor binding / negative regulation of systemic arterial blood pressure / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of programmed cell death / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / positive regulation of heterotypic cell-cell adhesion / positive regulation of protein-containing complex disassembly / positive regulation of podosome assembly / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / regulation of fat cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / response to L-glutamate / cortical actin cytoskeleton organization / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / prostaglandin metabolic process / regulation of synapse organization Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fox III, D. / Conrady, D.G. / Lowe, M. / Ceska, T. | ||||||
![]() | ![]() Title: A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF Authors: Lightwood, D.J. / Munro, R.J. / Porter, J. / McMillan, D. / Carrington, B. / Turner, A. / Scott-Tucker, A. / Hickford, E.S. / Schmidt, A. / Fox III, D. / Maloney, A. / Ceska, T. / Bourne, T. ...Authors: Lightwood, D.J. / Munro, R.J. / Porter, J. / McMillan, D. / Carrington, B. / Turner, A. / Scott-Tucker, A. / Hickford, E.S. / Schmidt, A. / Fox III, D. / Maloney, A. / Ceska, T. / Bourne, T. / O'Connell, J. / Lawson, A.D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.6 KB | Display | ![]() |
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PDB format | ![]() | 180.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 832.9 KB | Display | ![]() |
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Full document | ![]() | 840.9 KB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Tumor necrosis ... , 2 types, 5 molecules ABCFE
#1: Protein | Mass: 17457.736 Da / Num. of mol.: 3 / Mutation: N25D, C153S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 16196.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23649.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Antibody | Mass: 24066.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/NAG.gif)
#7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 30 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/D84.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D84.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-D84 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES, pH7.0, 10% w/v PEG6,000 and cryo-protected in glycerol performed in 5-10-15% steps. Vapor diffusion, sitting drop, temperature 289K PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2016 / Details: Beryllium Lenses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 32445 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 71.095 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.171 / Χ2: 0.958 / Net I/σ(I): 13.95 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: unpublished structure Resolution: 3→49.132 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.73 / 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: 175.92 Å2 / Biso mean: 69.5983 Å2 / Biso min: 23.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.132 Å
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Refine LS restraints |
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LS refinement shell |
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