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Yorodumi- PDB-3kfd: Ternary complex of TGF-b1 reveals isoform-specific ligand recogni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kfd | ||||||
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Title | Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily | ||||||
Components |
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Keywords | CYTOKINE/CYTOKINE RECEPTOR / TGF-beta / TGF-b1 / TGF-beta receptor type-1 / TGF-beta receptor type-2 / TbRII / TbRI / Growth factor / Receptor / Serine/threonine-protein kinase / CYTOKINE-CYTOKINE RECEPTOR complex | ||||||
Function / homology | Function and homology information positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / transforming growth factor beta receptor activity, type II / regulation of interleukin-23 production / bronchus morphogenesis / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / regulation of branching involved in mammary gland duct morphogenesis ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / transforming growth factor beta receptor activity, type II / regulation of interleukin-23 production / bronchus morphogenesis / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / regulation of branching involved in mammary gland duct morphogenesis / positive regulation of microglia differentiation / mammary gland morphogenesis / Influenza Virus Induced Apoptosis / lens fiber cell apoptotic process / frontal suture morphogenesis / growth plate cartilage chondrocyte growth / negative regulation of skeletal muscle tissue development / regulation of enamel mineralization / tricuspid valve morphogenesis / regulatory T cell differentiation / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / activin receptor activity / extracellular structure organization / epicardium morphogenesis / regulation of blood vessel remodeling / tolerance induction to self antigen / regulation of striated muscle tissue development / miRNA transport / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / columnar/cuboidal epithelial cell maturation / parathyroid gland development / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / positive regulation of odontogenesis / Langerhans cell differentiation / negative regulation of hyaluronan biosynthetic process / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / aorta morphogenesis / positive regulation of receptor signaling pathway via STAT / connective tissue replacement involved in inflammatory response wound healing / positive regulation of exit from mitosis / extracellular matrix assembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / odontoblast differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / transforming growth factor beta receptor activity / positive regulation of isotype switching to IgA isotypes / secondary palate development / positive regulation of mesenchymal stem cell proliferation / cardiac left ventricle morphogenesis / ventricular compact myocardium morphogenesis / mammary gland branching involved in thelarche / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / positive regulation of T cell tolerance induction / retina vasculature development in camera-type eye / heart valve morphogenesis / membranous septum morphogenesis / membrane protein intracellular domain proteolysis / response to laminar fluid shear stress / lung lobe morphogenesis / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / positive regulation of NK T cell differentiation / bronchiole development / hyaluronan catabolic process / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / activin receptor complex / neuron fate commitment / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / receptor catabolic process / lens fiber cell differentiation / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / oligodendrocyte development / TGFBR1 LBD Mutants in Cancer / receptor protein serine/threonine kinase / angiogenesis involved in coronary vascular morphogenesis / response to salt / transmembrane receptor protein serine/threonine kinase activity / germ cell migration / pharyngeal system development / negative regulation of biomineral tissue development / activin binding / myeloid dendritic cell differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å | ||||||
Authors | Radaev, S. / Sun, P.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Ternary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily. Authors: Radaev, S. / Zou, Z. / Huang, T. / Lafer, E.M. / Hinck, A.P. / Sun, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kfd.cif.gz | 237.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kfd.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfd ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | Hexamer |
-Components
#1: Protein | Mass: 12809.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Organ (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-lec3.2.8.1 / References: UniProt: P01137 #2: Protein | Mass: 13225.042 Da / Num. of mol.: 4 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P37173 #3: Protein | Mass: 9330.697 Da / Num. of mol.: 4 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P36897 #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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 8-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2007 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 23426 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.08 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1223 / Rsym value: 0.245 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2TGI, 1M9Z, 1REW Resolution: 2.995→46.08 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.763 / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 0.06 / Phase error: 30.61 / 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: 41.915 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.87 Å2 / Biso mean: 73.45 Å2 / Biso min: 16.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.995→46.08 Å
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Refine LS restraints |
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LS refinement shell |
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