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- PDB-3kfd: Ternary complex of TGF-b1 reveals isoform-specific ligand recogni... -
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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 | ||||||
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![]() | 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 | ![]() positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / regulation of branching involved in mammary gland duct morphogenesis / mammary gland morphogenesis ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / regulation of branching involved in mammary gland duct morphogenesis / mammary gland morphogenesis / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / lens fiber cell apoptotic process / frontal suture morphogenesis / growth plate cartilage chondrocyte growth / negative regulation of skeletal muscle tissue development / tricuspid valve morphogenesis / regulation of enamel mineralization / 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 / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / miRNA transport / 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 / membrane protein intracellular domain proteolysis / heart valve morphogenesis / endocardial cushion fusion / positive regulation of T cell tolerance induction / retina vasculature development in camera-type eye / membranous septum morphogenesis / response to laminar fluid shear stress / positive regulation of primary miRNA processing / lung lobe morphogenesis / positive regulation of NK T cell differentiation / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / bronchiole development / hyaluronan catabolic process / activin receptor activity, type I / regulation of transforming growth factor beta receptor signaling pathway / 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 / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / lens fiber cell differentiation / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / oligodendrocyte development / myeloid dendritic cell differentiation / receptor protein serine/threonine kinase / germ cell migration / angiogenesis involved in coronary vascular morphogenesis / response to salt / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / negative regulation of biomineral tissue development Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Radaev, S. / Sun, P.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.5 KB | Display | ![]() |
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PDB format | ![]() | 191.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523.8 KB | Display | ![]() |
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Full document | ![]() | 562.5 KB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 61.2 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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2 | ![]()
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3 |
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Unit cell |
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Details | Hexamer |
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Components
#1: Protein | Mass: 12809.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 13225.042 Da / Num. of mol.: 4 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 9330.697 Da / Num. of mol.: 4 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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