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- PDB-2l5s: Solution structure of the extracellular domain of the TGF-beta ty... -

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Basic information

Entry
Database: PDB / ID: 2l5s
TitleSolution structure of the extracellular domain of the TGF-beta type I receptor
ComponentsTGF-beta receptor type-1
KeywordsSIGNALING PROTEIN / ALK5 / transforming growth factor beta / type I receptor
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer ...extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / trophoblast cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / neuron fate commitment / activin receptor activity, type I / activin receptor complex / regulation of epithelial to mesenchymal transition / type II transforming growth factor beta receptor binding / pharyngeal system development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / TGFBR1 LBD Mutants in Cancer / germ cell migration / coronary artery morphogenesis / embryonic cranial skeleton morphogenesis / filopodium assembly / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / response to cholesterol / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / negative regulation of chondrocyte differentiation / lens development in camera-type eye / endothelial cell activation / anterior/posterior pattern specification / positive regulation of filopodium assembly / artery morphogenesis / skeletal system morphogenesis / ventricular septum morphogenesis / SMAD binding / negative regulation of endothelial cell proliferation / TGF-beta receptor signaling activates SMADs / roof of mouth development / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / regulation of protein ubiquitination / blastocyst development / bicellular tight junction / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / endothelial cell migration / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / Downregulation of TGF-beta receptor signaling / negative regulation of extrinsic apoptotic signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of apoptotic signaling pathway / post-embryonic development / skeletal system development / cell motility / kidney development / wound healing / peptidyl-serine phosphorylation / cellular response to growth factor stimulus / male gonad development / UCH proteinases / nervous system development / heart development / regulation of gene expression / positive regulation of cell growth / in utero embryonic development / protein kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome / regulation of cell cycle / intracellular signal transduction / Ub-specific processing proteases / cilium / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZuniga, J.E. / Ilangovan, U. / Pardeep, M. / Hinck, C. / Huang, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The TbetaR-I Pre-Helix Extension Is Structurally Ordered in the Unbound Form and Its Flanking Prolines Are Essential for Binding
Authors: Zuniga, J.E. / Ilangovan, U. / Mahlawat, P. / Hinck, C.S. / Huang, T. / Groppe, J.C. / McEwen, D.G. / Hinck, A.P.
History
DepositionNov 4, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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-1


Theoretical massNumber of molelcules
Total (without water)9,4731
Polymers9,4731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TGF-beta receptor type-1 / TGFR-1 / Activin receptor-like kinase 5 / ALK-5 / Serine/threonine-protein kinase receptor R4 / SKR4


Mass: 9472.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: P36897, receptor protein serine/threonine kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] TbRI-1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: TbRI-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.025 / pH: 7.2 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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