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- PDB-9f6x: Human transforming growth factor b type I receptor in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9f6x
TitleHuman transforming growth factor b type I receptor in complex with kinase inhibitor SB505124
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / TGF-beta Receptor type 1 in complex with SB505124
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / regulation of cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / myofibroblast differentiation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / trophoblast cell migration ...extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / regulation of cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / myofibroblast differentiation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / trophoblast cell migration / pharyngeal system development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / positive regulation of tight junction disassembly / positive regulation of extracellular matrix assembly / cardiac epithelial to mesenchymal transition / neuron fate commitment / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / activin receptor activity, type I / activin receptor complex / primordial germ cell migration / regulation of epithelial to mesenchymal transition / anterior/posterior pattern specification / receptor protein serine/threonine kinase / type II transforming growth factor beta receptor binding / activin binding / embryonic cranial skeleton morphogenesis / transmembrane receptor protein serine/threonine kinase activity / TGFBR1 LBD Mutants in Cancer / ventricular trabecula myocardium morphogenesis / coronary artery morphogenesis / activin receptor signaling pathway / collagen fibril organization / artery morphogenesis / skeletal system morphogenesis / negative regulation of chondrocyte differentiation / response to cholesterol / transforming growth factor beta binding / I-SMAD binding / endothelial cell activation / roof of mouth development / ventricular septum morphogenesis / thymus development / SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / regulation of protein ubiquitination / skeletal system development / cellular response to transforming growth factor beta stimulus / bicellular tight junction / transforming growth factor beta receptor signaling pathway / positive regulation of stress fiber assembly / positive regulation of epithelial to mesenchymal transition / kidney development / positive regulation of endothelial cell proliferation / in utero embryonic development / positive regulation of apoptotic signaling pathway / negative regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway / cell motility / wound healing / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / peptidyl-serine phosphorylation / cellular response to growth factor stimulus / heart development / regulation of gene expression / UCH proteinases / positive regulation of cell growth / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell cycle / protein kinase activity / signaling receptor complex / endosome / intracellular signal transduction / Ub-specific processing proteases / positive regulation of cell migration / membrane raft / ubiquitin protein ligase binding / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cell surface / signal transduction / ATP binding / membrane / metal ion binding / nucleus / plasma membrane
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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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
Similarity search - Domain/homology
: / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsRodriguez Buitrago, J.A. / Landstrom, M. / Wolf-Watz, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research CouncilFS 506-21 Sweden
Swedish Research Council2021-04513_VR Sweden
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Human transforming growth factor beta type I receptor in complex with kinase inhibitor SB505124.
Authors: Rodriguez Buitrago, J.A. / Landstrom, M. / Wolf-Watz, M.
History
DepositionMay 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0854
Polymers34,5661
Non-polymers5203
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-0 kcal/mol
Surface area14780 Å2
Unit cell
Length a, b, c (Å)42.070, 79.846, 87.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGF-beta receptor type-1 / TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ...TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ALK-5 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TbetaR-I


Mass: 34565.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Plasmid: pFastBac / Cell line (production host): fS9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): fS9
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-A1IAZ / 2-[5-(1,3-benzodioxol-5-yl)-2-~{tert}-butyl-1~{H}-imidazol-4-yl]-6-methyl-pyridine


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6 / Details: 23%(w/v) PEG 3350, 3%(v/v) glycerol at pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Jul 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→59.07 Å / Num. obs: 12847 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.997 / Net I/σ(I): 8.2
Reflection shellResolution: 2.68→2.74 Å / Num. unique obs: 8038 / CC1/2: 0.36 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
STARANISOdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→10.87 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.719 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 404 4.8 %RANDOM
Rwork0.21223 ---
obs0.21399 8038 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.776 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0 Å2
2--0.87 Å2-0 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.68→10.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 37 93 2555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122514
X-RAY DIFFRACTIONr_bond_other_d0.0050.0162390
X-RAY DIFFRACTIONr_angle_refined_deg2.2411.8233394
X-RAY DIFFRACTIONr_angle_other_deg1.1951.785484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8445302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.417.22227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47710446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022998
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6741.2271211
X-RAY DIFFRACTIONr_mcbond_other0.6741.2251210
X-RAY DIFFRACTIONr_mcangle_it1.232.2251512
X-RAY DIFFRACTIONr_mcangle_other1.232.2281513
X-RAY DIFFRACTIONr_scbond_it0.6481.281303
X-RAY DIFFRACTIONr_scbond_other0.6481.2811304
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1422.3321883
X-RAY DIFFRACTIONr_long_range_B_refined4.68612.212662
X-RAY DIFFRACTIONr_long_range_B_other4.62112.212654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 22 -
Rwork0.239 510 -
obs--88.37 %
Refinement TLS params.Method: refined / Origin x: -9.2499 Å / Origin y: 1.7799 Å / Origin z: -12.3269 Å
111213212223313233
T0.0622 Å2-0.0328 Å20.0193 Å2-0.1511 Å2-0.1608 Å2--0.1895 Å2
L4.6782 °2-0.7698 °20.0112 °2-2.7113 °21.0799 °2--1.8321 °2
S0.0107 Å °0.6897 Å °-0.8985 Å °-0.0917 Å °-0.0443 Å °0.1366 Å °0.1527 Å °-0.0521 Å °0.0336 Å °

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