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- PDB-5e8t: TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) -

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Basic information

Entry
Database: PDB / ID: 5e8t
TitleTGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D)
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / ALK5 / SB431542 / KINASE DOMAIN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
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 / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...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 / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / TGFBR3 regulates TGF-beta signaling / regulation of epithelial to mesenchymal transition / positive regulation of tight junction disassembly / activin receptor complex / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of vasculature development / neuron fate commitment / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor activity, type I / type II transforming growth factor beta receptor binding / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / angiogenesis involved in coronary vascular morphogenesis / transforming growth factor beta receptor activity, type III / TGFBR1 LBD Mutants in Cancer / activin binding / coronary artery morphogenesis / germ cell migration / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / response to cholesterol / embryonic cranial skeleton morphogenesis / I-SMAD binding / transforming growth factor beta binding / negative regulation of chondrocyte differentiation / collagen fibril organization / lens development in camera-type eye / endothelial cell activation / skeletal system morphogenesis / anterior/posterior pattern specification / positive regulation of filopodium assembly / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / negative regulation of endothelial cell proliferation / TGF-beta receptor signaling activates SMADs / blastocyst development / positive regulation of SMAD protein signal transduction / endothelial cell migration / regulation of protein ubiquitination / epithelial to mesenchymal transition / bicellular tight junction / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / post-embryonic development / Downregulation of TGF-beta receptor signaling / negative regulation of cell migration / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / skeletal system development / kidney development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / cell motility / wound healing / cellular response to growth factor stimulus / male gonad development / UCH proteinases / heart development / nervous system development / regulation of gene expression / peptidyl-serine phosphorylation / positive regulation of cell growth / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / regulation of cell cycle / protein kinase activity / endosome / intracellular signal transduction / Ub-specific processing proteases / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process
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 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...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 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSheriff, S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structures of apo and inhibitor-bound TGF beta R2 kinase domain: insights into TGF beta R isoform selectivity.
Authors: Tebben, A.J. / Ruzanov, M. / Gao, M. / Xie, D. / Kiefer, S.E. / Yan, C. / Newitt, J.A. / Zhang, L. / Kim, K. / Lu, H. / Kopcho, L.M. / Sheriff, S.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4424
Polymers35,1651
Non-polymers2763
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-1 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.790, 77.380, 89.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TbetaR-I


Mass: 35165.473 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 200-503 / Mutation: T204D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Plasmid: PFASTBAC1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 23%(w/v) PEG3350, 3%(v/v) glcyerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2014 / Details: KIRKPATRICK-BAEZ
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.79 Å / Num. obs: 32423 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.78 Å2 / Rsym value: 0.076 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.96 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.6 / Rejects: 0 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZM

3tzm


Resolution: 1.7→22.4 Å / Cor.coef. Fo:Fc: 0.9569 / Cor.coef. Fo:Fc free: 0.9536 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 1631 5.04 %RANDOM
Rwork0.1686 ---
obs0.1697 32352 99.14 %-
Displacement parametersBiso max: 97.63 Å2 / Biso mean: 22.29 Å2 / Biso min: 9.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.9834 Å20 Å20 Å2
2---3.4234 Å20 Å2
3---1.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.166 Å
Refinement stepCycle: final / Resolution: 1.7→22.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 18 217 2626
Biso mean--41.68 29.61 -
Num. residues----302
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d875SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes362HARMONIC5
X-RAY DIFFRACTIONt_it2464HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion321SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3076SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2464HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3330HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.05
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2275 138 5.06 %
Rwork0.2018 2589 -
all0.2031 2727 -
obs--99.14 %

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