+Open data
-Basic information
Entry | Database: PDB / ID: 3alq | ||||||
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Title | Crystal structure of TNF-TNFR2 complex | ||||||
Components |
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Keywords | CYTOKINE/CYTOKINE RECEPTOR / LIGAND-RECEPTOR COMPLEX / CYTOKINE / CYTOKINE-CYTOKINE RECEPTOR complex | ||||||
Function / homology | Function and homology information glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / 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 ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / 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 / aortic valve development / positive regulation of leukocyte adhesion to arterial endothelial cell / tumor necrosis factor receptor activity / positive regulation of vitamin D biosynthetic process / negative regulation of extracellular matrix constituent secretion / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / regulation of endothelial cell apoptotic process / regulation of T cell cytokine production / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / varicosity / positive regulation of humoral immune response mediated by circulating immunoglobulin / response to gold nanoparticle / negative regulation of neuroinflammatory response / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of amyloid-beta clearance / tumor necrosis factor binding / TNFs bind their physiological receptors / 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 / negative regulation of cardiac muscle hypertrophy / cellular response to toxic substance / positive regulation of myelination / 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 / regulation of neuroinflammatory response / 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 / regulation of myelination / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of heart rate Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Mukai, Y. / Nakamura, T. / Yamagata, Y. / Tsutsumi, Y. | ||||||
Citation | Journal: Sci.Signal. / Year: 2010 Title: Solution of the Structure of the TNF-TNFR2 Complex Authors: Mukai, Y. / Nakamura, T. / Yoshikawa, M. / Yoshioka, Y. / Tsunoda, S.I. / Nakagawa, S. / 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 | 3alq.cif.gz | 350.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3alq.ent.gz | 286.7 KB | Display | PDB format |
PDBx/mmJSON format | 3alq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3alq ftp://data.pdbj.org/pub/pdb/validation_reports/al/3alq | HTTPS FTP |
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-Related structure data
Related structure data | 2e7aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17279.377 Da / Num. of mol.: 6 / Fragment: soluble form / Mutation: K11M, K65S, K90P, K98R, K112N, K128P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (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: Protein | Mass: 18785.223 Da / Num. of mol.: 6 / Fragment: residues in UNP 33-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFBR, TNFR2, TNFRSF1B / Plasmid: PYAS (MODIFIED FROM PUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20333 #3: Chemical | ChemComp-CO / #4: 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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 45945 / % possible obs: 98.9 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 2.95→3.06 Å / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.51 / Num. unique all: 4075 / % possible all: 89.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2e7a Resolution: 3→49.96 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 28.49 / 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 / Bsol: 25.479 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→49.96 Å
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Refine LS restraints |
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LS refinement shell |
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