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- PDB-1ktz: Crystal Structure of the Human TGF-beta Type II Receptor Extracel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ktz | ||||||
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Title | Crystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex with TGF-beta3 | ||||||
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![]() | CYTOKINE/CYTOKINE RECEPTOR / CYTOKINE-RECEPTOR COMPLEX / 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 / uterine wall breakdown / bronchus morphogenesis / detection of hypoxia / mammary gland morphogenesis / lens fiber cell apoptotic process / frontal suture 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 / uterine wall breakdown / bronchus morphogenesis / detection of hypoxia / mammary gland morphogenesis / lens fiber cell apoptotic process / frontal suture morphogenesis / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / embryonic neurocranium morphogenesis / activin receptor activity / miRNA transport / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / Langerhans cell differentiation / positive regulation of tight junction disassembly / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / secondary palate development / cardiac left ventricle morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / positive regulation of T cell tolerance induction / membranous septum morphogenesis / response to laminar fluid shear stress / lung lobe morphogenesis / positive regulation of NK T cell differentiation / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / mammary gland development / SMAD protein signal transduction / regulation of stem cell differentiation / cell-cell junction organization / glycosaminoglycan binding / kinase activator activity / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / digestive tract development / aortic valve morphogenesis / face morphogenesis / odontogenesis / lens development in camera-type eye / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of filopodium assembly / positive regulation of mesenchymal cell proliferation / trachea formation / artery morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / lung alveolus development / activation of protein kinase activity / roof of mouth development / positive regulation of epithelial cell migration / blood vessel development / heart looping / outflow tract morphogenesis / SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of SMAD protein signal transduction / inner ear development / positive regulation of cell division / ECM proteoglycans / positive regulation of collagen biosynthetic process / epithelial to mesenchymal transition / vasculogenesis / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / gastrulation / Notch signaling pathway / positive regulation of stress fiber assembly / T-tubule / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / platelet alpha granule lumen / cytokine activity / caveola / response to progesterone / female pregnancy Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hart, P.J. / Deep, S. / Taylor, A.B. / Shu, Z. / Hinck, C.S. / Hinck, A.P. | ||||||
![]() | ![]() Title: Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex. Authors: Hart, P.J. / Deep, S. / Taylor, A.B. / Shu, Z. / Hinck, C.S. / Hinck, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.5 KB | Display | ![]() |
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PDB format | ![]() | 39.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the crystallographic symmetry operator y, x, -z and a translation of one unit cell length along the z-axis. |
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Components
#1: Protein | Mass: 12734.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13853.632 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||||||
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Crystal grow | Details: HANGING DROP VAPOR DIFFUSION USING A WELL SOLUTION CONTAINING 20% (V/V) 2-METHYL-2,4-PENTANEDIOL AND 0.1 M CITRATE PH 4.0 | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 75 % | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→26 Å / Num. all: 29006 / Num. obs: 29006 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2824 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 154181 |
Reflection shell | *PLUS % possible obs: 98.8 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.0368 Å2 / ksol: 0.356719 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→25.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 26 Å / σ(F): 0 / % reflection Rfree: 6.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.288 / % reflection Rfree: 7.1 % / Rfactor Rwork: 0.265 |