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- PDB-8yhf: The Crystal Structure of the Type I TGF beta receptor from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8yhf
TitleThe Crystal Structure of the Type I TGF beta receptor from Biortus.
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / Serine/threonine-protein kinase / apoptosis / ATP-binding
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / regulation of cardiac muscle cell proliferation / transforming growth factor beta ligand-receptor complex / 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 / regulation of cardiac muscle cell proliferation / transforming growth factor beta ligand-receptor complex / 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 / trophoblast cell migration / 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 extracellular matrix assembly / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / mesenchymal cell differentiation / TGFBR3 regulates TGF-beta signaling / neuron fate commitment / positive regulation of vasculature development / activin receptor activity, type I / activin receptor complex / regulation of epithelial to mesenchymal transition / pharyngeal system development / type II transforming growth factor beta receptor binding / receptor protein serine/threonine kinase / activin binding / transmembrane receptor protein serine/threonine kinase activity / TGFBR1 LBD Mutants in Cancer / primordial germ cell migration / embryonic cranial skeleton morphogenesis / coronary artery morphogenesis / filopodium assembly / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / response to cholesterol / transforming growth factor beta binding / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / lens development in camera-type eye / anterior/posterior pattern specification / endothelial cell activation / artery morphogenesis / positive regulation of filopodium assembly / skeletal system morphogenesis / ventricular septum morphogenesis / negative regulation of endothelial cell proliferation / SMAD binding / roof of mouth development / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / regulation of protein ubiquitination / epithelial to mesenchymal transition / bicellular tight junction / blastocyst development / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / endothelial cell migration / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / ciliary tip / thymus development / negative regulation of cell migration / peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway / post-embryonic development / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / skeletal system development / positive regulation of apoptotic signaling pathway / kidney development / wound healing / cell motility / cellular response to growth factor stimulus / male gonad development / UCH proteinases / nervous system development / heart development / positive regulation of cell growth / regulation of gene expression / in utero embryonic development / protein kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor complex / endosome / regulation of cell cycle / Ub-specific processing proteases / intracellular signal transduction / cilium / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation
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: 1.4 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of the Type I TGF beta receptor from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_contact_author.email / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,3772
Polymers38,9781
Non-polymers3991
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.196, 76.764, 89.707
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 / 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: 38977.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-A1D6I / Vactosertib


Mass: 399.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18FN7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M K/Na PO4, 0.1M Bis-Tris propane pH6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.85 Å / Num. obs: 56084 / % possible obs: 96.4 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 2705 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.757 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.028 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1924 2711 4.839 %
Rwork0.1661 53314 -
all0.167 --
obs-56025 96.251 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.403 Å2-0 Å2-0 Å2
2--1.147 Å2-0 Å2
3----0.744 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 30 351 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122565
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162453
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6563487
X-RAY DIFFRACTIONr_angle_other_deg0.4291.5845643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.525.53628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85210468
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.56910121
X-RAY DIFFRACTIONr_chiral_restr0.0640.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2150.2468
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22188
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21231
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.27
X-RAY DIFFRACTIONr_nbd_other0.1650.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.220
X-RAY DIFFRACTIONr_mcbond_it1.3081.8371219
X-RAY DIFFRACTIONr_mcbond_other1.3071.8371219
X-RAY DIFFRACTIONr_mcangle_it2.0833.2991529
X-RAY DIFFRACTIONr_mcangle_other2.0823.3031530
X-RAY DIFFRACTIONr_scbond_it1.9782.0761346
X-RAY DIFFRACTIONr_scbond_other1.9772.0751347
X-RAY DIFFRACTIONr_scangle_it3.213.6981944
X-RAY DIFFRACTIONr_scangle_other3.2093.6971945
X-RAY DIFFRACTIONr_lrange_it4.96821.1613025
X-RAY DIFFRACTIONr_lrange_other4.72618.7192931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.2551930.24738170.24742600.9550.9694.13150.213
1.436-1.4760.2651800.22737180.22841170.9530.96594.68060.192
1.476-1.5180.2341810.20735970.20840280.9590.9793.79340.17
1.518-1.5650.2081700.19635450.19739280.9710.97494.57740.164
1.565-1.6160.2191690.1834560.18137820.9670.97895.84880.151
1.616-1.6730.2051930.17533160.17736730.9740.9895.5350.147
1.673-1.7360.2021790.16532070.16735420.9730.98295.59570.143
1.736-1.8070.1981730.17331170.17434250.9740.98196.05840.152
1.807-1.8870.1771460.1630090.16132710.9780.98496.45370.143
1.887-1.9790.1871480.16729010.16831540.9770.98396.67090.155
1.979-2.0850.191430.15827850.1630200.9790.98596.95360.15
2.085-2.2110.1641250.15326340.15328440.9830.98797.01130.149
2.211-2.3640.1771110.15825210.15826950.9790.98497.66230.157
2.364-2.5520.1941220.1523340.15224950.9790.98598.43690.155
2.552-2.7950.1961120.16421680.16623250.9760.98298.06450.175
2.795-3.1220.221990.16619690.16920990.9690.98298.52310.182
3.122-3.6020.171850.14817770.14918870.9820.98798.67510.17
3.602-4.4010.177790.14815130.14916080.9810.98699.0050.176
4.401-6.1850.181670.17512000.17512780.9810.98699.13930.212
6.185-38.7570.206360.2047300.2047740.9660.97798.96640.242

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