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- PDB-1ks6: Transforming Growth Factor Beta type II receptor ligand binding domain -

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Basic information

Entry
Database: PDB / ID: 1ks6
TitleTransforming Growth Factor Beta type II receptor ligand binding domain
ComponentsTRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR
KeywordsHORMONE/GROWTH FACTOR / THREE FINGER TOXIN FOLD / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


TGF-beta receptor signaling activates SMADs / TGFBR3 regulates TGF-beta signaling / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / activin receptor activity / detection of hypoxia / type III transforming growth factor beta receptor binding / negative regulation of macrophage cytokine production / transforming growth factor beta receptor activity / positive regulation of tight junction disassembly ...TGF-beta receptor signaling activates SMADs / TGFBR3 regulates TGF-beta signaling / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / activin receptor activity / detection of hypoxia / type III transforming growth factor beta receptor binding / negative regulation of macrophage cytokine production / transforming growth factor beta receptor activity / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / eye development / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / cell activation / transforming growth factor beta receptor activity, type III / activin binding / pattern specification process / type I transforming growth factor beta receptor binding / glycosaminoglycan binding / cell-cell junction organization / response to cholesterol / transforming growth factor beta binding / face morphogenesis / SMAD binding / embryonic organ development / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / extracellular matrix / transforming growth factor beta receptor signaling pathway / response to progesterone / positive regulation of protein secretion / lung development / cellular response to growth factor stimulus / caveola / positive regulation of reactive oxygen species metabolic process / cell migration / heart development / response to hypoxia / receptor complex / positive regulation of cell migration / protein phosphorylation / membrane raft / response to xenobiotic stimulus / external side of plasma membrane / apoptotic process / positive regulation of gene expression / ATP binding / metal ion binding / membrane / plasma membrane
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMarlow, M.S. / Brown, C.B. / Barnett, J.V. / Krezel, A.M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution structure of the chick TGFb type II receptor ligand binding domain
Authors: Marlow, M.S. / Brown, C.B. / Barnett, J.V. / Krezel, A.M.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR


Theoretical massNumber of molelcules
Total (without water)12,0671
Polymers12,0671
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)20 / 100target function
RepresentativeModel #6closest to the average

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Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR / TGFb type II receptor


Mass: 12066.688 Da / Num. of mol.: 1
Fragment: LIGAND BINDING DOMAIN, SEQUENCE DATABASE RESIDUES 34-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q90999
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
142HNCA-J

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM TbRII Natural Abundance100% D2O
21-2mM TbRII U-15N,13C90% H2O/10% D2O
31-2mM TbRII U-15N,13C100% D2O
Sample conditionsIonic strength: 1 / pH: 6.5 / Pressure: ambient / Temperature: 300 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 AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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