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- PDB-1plo: TRANSFORMING GROWTH FACTOR-BETA TYPE II RECEPTOR EXTRACELLULAR DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1plo
TitleTRANSFORMING GROWTH FACTOR-BETA TYPE II RECEPTOR EXTRACELLULAR DOMAIN
ComponentsTGF-beta receptor type II
KeywordsCytokine receptor / Three-Finger Toxin Fold
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 / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer ...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 / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / activin receptor activity / miRNA transport / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / Langerhans cell differentiation / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / 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 / lung lobe morphogenesis / positive regulation of NK T cell differentiation / 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 / SMAD protein signal transduction / regulation of stem cell differentiation / glycosaminoglycan binding / kinase activator activity / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / aortic valve morphogenesis / lens development in camera-type eye / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / trachea formation / artery morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / 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 / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / vasculogenesis / positive regulation of epithelial to mesenchymal transition / gastrulation / Notch signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / caveola / brain development / cellular response to growth factor stimulus / positive regulation of angiogenesis / UCH proteinases / positive regulation of reactive oxygen species metabolic process / heart development / regulation of cell population proliferation / regulation of gene expression / in utero embryonic development / molecular adaptor activity / receptor complex / response to xenobiotic stimulus / membrane raft / phosphorylation / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / extracellular space / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / substructure distance geometry, full structure distance geometry-simulated annealing; torsion angle dynamics
AuthorsDeep, S. / Walker III, K.P. / Shu, Z. / Hinck, A.P.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure and backbone dynamics of the TGF-beta type II receptor extracellular domain
Authors: Deep, S. / Walker III, K.P. / Shu, Z. / Hinck, A.P.
History
DepositionJun 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type II


Theoretical massNumber of molelcules
Total (without water)13,8111
Polymers13,8111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1fewest violations, lowest energy

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Components

#1: Protein TGF-beta receptor type II / TGFR-2 / TGF-beta type II receptor


Mass: 13810.606 Da / Num. of mol.: 1 / Mutation: N19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37173, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2233D 13C-separated NOESY
2334D 13C-separated NOESY
1423D 15N edited, 13C-edited 1H-1H NOESY
1513D 15N-edited,15N-edited 1H-1H NOESY
3641H-15H 1-bond residual dipolar coupling (2D IPAP-HSQC)
37513C-13CO residual dipolar coupling (3D (HA)CA(CO)NH
38513Calpha-13CO residual dipolar coupling (3D Ca-coupled HNCO)
NMR detailsText: This structure was determined by refining simultaneously against NOE, J-coupling, dihedral angle, and residual dipolar coupling constraints

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM ecTbR2 U-15N, 25mM sodium acetate, 25mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
21mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
31mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 99.99% D2O99.99% D2O
41mM ecTbR2 U-15N, 25mM sodium acetate, 25mM NaCl, 4% (w/v) 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14-O-PC) mixed in a molar ratio of 1:3, 95% H2O, 5% D2O95% H2O/5% D2O
51mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 4% (w/v) 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14-O-PC) mixed in a molar ratio of 1:3, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM sodium acetate, 25mM NaCl, pH 5.5 5.5 ambient 300 K
225mM sodium acetate, 25mM NaCl 5.1 ambient 300 K
325mM sodium acetate, 25mM NaCl 5.5 ambient 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR softwareName: XPLOR_NIH / Version: 1.06
Developer: Clore, G.M., Kuszewski, J., Schwieters, C.D., Tjandra, N.
Classification: refinement
RefinementMethod: substructure distance geometry, full structure distance geometry-simulated annealing; torsion angle dynamics
Software ordinal: 1
Details: structures are based on a total of 1583 constraints, 1168 are NOE distance, 138 are dihedredral angle, 58 are 3JHNHa coupling constant, 219 are residual dipolar couplings,
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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