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- PDB-2pjy: Structural basis for cooperative assembly of the TGF-beta signali... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pjy | ||||||
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Title | Structural basis for cooperative assembly of the TGF-beta signaling complex | ||||||
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![]() | CYTOKINE/CYTOKINE RECEPTOR / ternary complex / three finger toxin / 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 / extracellular structure organization / epicardium morphogenesis / miRNA transport / parathyroid gland development / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / Langerhans cell differentiation / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / myofibroblast differentiation / 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 / positive regulation of mesenchymal stem cell proliferation / cardiac left ventricle morphogenesis / ventricular compact myocardium 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 / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / 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 / positive regulation of extracellular matrix assembly / 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 / germ cell migration / angiogenesis involved in coronary vascular morphogenesis / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / type I transforming growth factor beta receptor binding / coronary artery morphogenesis / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / mammary gland development / activin receptor signaling pathway / SMAD protein signal transduction / regulation of stem cell differentiation / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / filopodium assembly / glycosaminoglycan binding / kinase activator activity / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / digestive tract development / I-SMAD binding / aortic valve morphogenesis / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / face morphogenesis / odontogenesis / endothelial cell proliferation / lens development in camera-type eye / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of filopodium assembly / anterior/posterior pattern specification / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Groppe, J. / Zubieta, C. | ||||||
![]() | ![]() Title: Cooperative assembly of TGF-beta superfamily signaling complexes is mediated by two disparate mechanisms and distinct modes of receptor binding. Authors: Groppe, J. / Hinck, C.S. / Samavarchi-Tehrani, P. / Zubieta, C. / Schuermann, J.P. / Taylor, A.B. / Schwarz, P.M. / Wrana, J.L. / 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 | ![]() | 71.3 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 439.8 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ktzS S: Starting model for refinement |
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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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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: 12244.113 Da / Num. of mol.: 1 / Fragment: extracellular domain / Mutation: N42A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P37173, receptor protein serine/threonine kinase |
#3: Protein | Mass: 8715.943 Da / Num. of mol.: 1 / Fragment: extracellular domain / Mutation: M70S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36897, receptor protein serine/threonine kinase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-20% PEG 3350, 0.4-0.65 M calcium acetate, 0.1-0.25M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 6710 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 75.056 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.078 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 3→3.29 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 17731 / Num. unique all: 1724 / Rsym value: 0.63 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.525 / Cor.coef. Fo:Fc: 0.267
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1KTZ Resolution: 3→28.8 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 63.761 / SU ML: 0.508 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.645 Å2
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Refinement step | Cycle: LAST / Resolution: 3→28.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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