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- PDB-4p7u: Extracellular domain of type II Transforming Growth Factor Beta r... -

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Basic information

Entry
Database: PDB / ID: 4p7u
TitleExtracellular domain of type II Transforming Growth Factor Beta receptor in complex with NDSB-201
ComponentsTGF-beta receptor type-2
KeywordsSIGNALING PROTEIN / NDSB-201 / type II Transforming Growth Factor Beta receptor
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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.502 Å
AuthorsWangkanont, K. / Forest, K.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055984 United States
CitationJournal: Protein Expr.Purif. / Year: 2015
Title: The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to promote folding and crystallization of the type II TGF-beta receptor extracellular domain.
Authors: Wangkanont, K. / Forest, K.T. / Kiessling, L.L.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9572
Polymers12,7551
Non-polymers2011
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint6 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.574, 40.463, 75.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein TGF-beta receptor type-2 / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TbetaR-II


Mass: 12755.442 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 74-175 / Mutation: Q26A K97T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P37173, receptor protein serine/threonine kinase
#2: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.044 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium citrate, 30% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→22.1 Å / Num. obs: 17064 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.96 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.063 / Net I/av σ(I): 33.32 / Net I/σ(I): 11.9 / Num. measured all: 104863
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.556.10.41916530.74898.5
1.55-1.626.20.31516510.81398.8
1.62-1.696.20.23316760.87499.2
1.69-1.786.30.16616760.92599.4
1.78-1.896.30.12216650.97499.7
1.89-2.046.10.09217061.29499.8
2.04-2.246.20.07417211.35699.9
2.24-2.566.30.05417071.125100
2.56-3.236.20.04417471.122100
3.23-22.15.70.04118621.37399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.66 Å21.44 Å
Translation4.66 Å21.44 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
DENZOdata reduction
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M9Z

1m9z


Resolution: 1.502→21.439 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 1703 10.01 %random selection
Rwork0.1705 15317 --
obs0.174 17020 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.73 Å2 / Biso mean: 22.3415 Å2 / Biso min: 8.33 Å2
Refinement stepCycle: final / Resolution: 1.502→21.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 26 90 913
Biso mean--36.2 34.61 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007949
X-RAY DIFFRACTIONf_angle_d1.1811286
X-RAY DIFFRACTIONf_chiral_restr0.081136
X-RAY DIFFRACTIONf_plane_restr0.005170
X-RAY DIFFRACTIONf_dihedral_angle_d14.485370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.502-1.54580.24181350.19441214134997
1.5458-1.59560.22461410.18051277141899
1.5956-1.65260.17981380.164412281366100
1.6526-1.71880.22781370.18181239137699
1.7188-1.7970.20151400.1721259139999
1.797-1.89170.2221390.174412621401100
1.8917-2.01010.21181430.161412831426100
2.0101-2.16520.19621420.165112691411100
2.1652-2.38280.20231440.170913011445100
2.3828-2.7270.22451420.177312821424100
2.727-3.43350.21591470.173713131460100
3.4335-21.44120.18931550.165113901545100

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