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Open data
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Basic information
Entry | Database: PDB / ID: 6mac | ||||||
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Title | Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD | ||||||
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![]() | SIGNALING PROTEIN / Growth Factor / Receptor / TGFB / Signaling | ||||||
Function / homology | ![]() spinal cord anterior/posterior patterning / type B pancreatic cell maturation / Signaling by BMP / negative regulation of amacrine cell differentiation / inhibin binding / activin receptor activity, type II / amacrine cell differentiation / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / Signaling by BMP / negative regulation of amacrine cell differentiation / inhibin binding / activin receptor activity, type II / amacrine cell differentiation / lymphatic endothelial cell differentiation / positive regulation of activin receptor signaling pathway / activin receptor activity / extracellular structure organization / epicardium morphogenesis / venous blood vessel development / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / myofibroblast differentiation / Signaling by Activin / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / lymphangiogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / sexual reproduction / retina vasculature development in camera-type eye / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / embryonic foregut morphogenesis / 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 / TGFBR1 LBD Mutants in Cancer / camera-type eye morphogenesis / artery development / receptor protein serine/threonine kinase / pattern specification process / germ cell migration / angiogenesis involved in coronary vascular morphogenesis / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / SMAD protein signal transduction / ventricular trabecula myocardium morphogenesis / filopodium assembly / metanephros development / kinase activator activity / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / gastrulation with mouth forming second / I-SMAD binding / collagen fibril organization / pancreas development / negative regulation of chondrocyte differentiation / determination of left/right symmetry / endothelial cell activation / skeletal system morphogenesis / negative regulation of cold-induced thermogenesis / insulin secretion / endothelial cell proliferation / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ureteric bud development / organ growth / adrenal gland development / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / growth factor binding / negative regulation of endothelial cell proliferation / odontogenesis of dentin-containing tooth / mesoderm development / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / regulation of signal transduction / bicellular tight junction / epithelial to mesenchymal transition / blood vessel remodeling / BMP signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / response to glucose / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goebel, E.J. / Thompson, T.B. | ||||||
![]() | ![]() Title: Structural characterization of an activin class ternary receptor complex reveals a third paradigm for receptor specificity. Authors: Goebel, E.J. / Corpina, R.A. / Hinck, C.S. / Czepnik, M. / Castonguay, R. / Grenha, R. / Boisvert, A. / Miklossy, G. / Fullerton, P.T. / Matzuk, M.M. / Idone, V.J. / Economides, A.N. / ...Authors: Goebel, E.J. / Corpina, R.A. / Hinck, C.S. / Czepnik, M. / Castonguay, R. / Grenha, R. / Boisvert, A. / Miklossy, G. / Fullerton, P.T. / Matzuk, M.M. / Idone, V.J. / Economides, A.N. / Kumar, R. / Hinck, A.P. / Thompson, T.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
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PDB format | ![]() | 52.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 15.8 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12357.206 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 11244.370 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P38445, receptor protein serine/threonine kinase | ||
#3: Protein | Mass: 8857.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36897, receptor protein serine/threonine kinase | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.09 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: .05-.15M sodium acetate 12-24% polyethylene glycol 8000 .05-.15M sodium thiocyanate PH range: 4.5-6.3 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033202 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50.5 Å / Num. obs: 18669 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 66.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0269 / Rpim(I) all: 0.0269 / Rrim(I) all: 0.038 / Net I/σ(I): 12.07 |
Reflection shell | Resolution: 2.34→2.424 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4022 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1861 / CC1/2: 0.455 / Rpim(I) all: 0.4022 / Rrim(I) all: 0.5687 / % possible all: 99.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E4G, 3KFD, 1NYS Resolution: 2.34→50.5 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 32.27 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.65 Å2 / Biso mean: 73.7106 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.34→50.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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