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- PDB-8yhl: The Crystal Structure of Tgf-Beta Type I Receptor (Alk5) from Biortus -

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Basic information

Entry
Database: PDB / ID: 8yhl
TitleThe Crystal Structure of Tgf-Beta Type I Receptor (Alk5) 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 / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / 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 / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / germ cell migration / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / filopodium assembly / ventricular trabecula myocardium morphogenesis / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / negative regulation of chondrocyte differentiation / collagen fibril organization / endothelial cell proliferation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / TGF-beta receptor signaling activates SMADs / SMAD binding / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of apoptotic signaling pathway / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / post-embryonic development / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / skeletal system development / cell motility / negative regulation of extrinsic apoptotic signaling pathway / wound healing / 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 / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / regulation of cell cycle / Ub-specific processing proteases / endosome / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
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
: / ACETATE ION / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 Tgf-Beta Type I Receptor (Alk5) 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

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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)35,5816
Polymers34,9391
Non-polymers6425
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.813, 77.464, 89.524
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: 34939.199 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 / 2-fluoranyl-~{N}-[[5-(6-methylpyridin-2-yl)-4-([1,2,4]triazolo[1,5-a]pyridin-6-yl)-1~{H}-imidazol-2-yl]methyl]aniline / Vactosertib


Mass: 399.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18FN7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MgAC2, 0.1M MES pH6.5, 10% PEG10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18067 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18067 Å / Relative weight: 1
ReflectionResolution: 1.47→44.76 Å / Num. obs: 50369 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 1.47→1.5 Å / Num. unique obs: 2526 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→38.762 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.32 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1932 2460 4.89 %
Rwork0.1634 47842 -
all0.165 --
obs-50302 99.96 %
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: 18.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.353 Å2-0 Å20 Å2
2--0.288 Å2-0 Å2
3---0.066 Å2
Refinement stepCycle: LAST / Resolution: 1.47→38.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 46 351 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152449
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6393487
X-RAY DIFFRACTIONr_angle_other_deg1.4851.5835623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23120.959146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2631524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
X-RAY DIFFRACTIONr_nbd_refined0.220.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22366
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21264
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.218
X-RAY DIFFRACTIONr_nbd_other0.2160.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.225
X-RAY DIFFRACTIONr_mcbond_it1.5541.7191233
X-RAY DIFFRACTIONr_mcbond_other1.4911.7151230
X-RAY DIFFRACTIONr_mcangle_it2.0782.5771541
X-RAY DIFFRACTIONr_mcangle_other2.082.5791542
X-RAY DIFFRACTIONr_scbond_it2.5171.9511343
X-RAY DIFFRACTIONr_scbond_other2.5161.9521344
X-RAY DIFFRACTIONr_scangle_it3.8272.8221938
X-RAY DIFFRACTIONr_scangle_other3.8262.8231939
X-RAY DIFFRACTIONr_lrange_it5.32521.513114
X-RAY DIFFRACTIONr_lrange_other5.14920.9173038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.5080.2691670.2653509X-RAY DIFFRACTION99.9185
1.508-1.5490.2521750.2353441X-RAY DIFFRACTION100
1.549-1.5940.2511520.2153302X-RAY DIFFRACTION100
1.594-1.6430.2621730.2093189X-RAY DIFFRACTION99.9405
1.643-1.6970.2011510.193128X-RAY DIFFRACTION99.9695
1.697-1.7570.2131800.1773005X-RAY DIFFRACTION99.9686
1.757-1.8230.1881460.1692930X-RAY DIFFRACTION100
1.823-1.8970.1811430.1652817X-RAY DIFFRACTION100
1.897-1.9820.211300.1642705X-RAY DIFFRACTION100
1.982-2.0780.1791400.1632583X-RAY DIFFRACTION100
2.078-2.1910.1981220.1592474X-RAY DIFFRACTION99.9615
2.191-2.3230.1991360.1522332X-RAY DIFFRACTION100
2.323-2.4830.1811260.1422182X-RAY DIFFRACTION100
2.483-2.6820.1911000.1522056X-RAY DIFFRACTION99.9536
2.682-2.9370.1681060.1481900X-RAY DIFFRACTION100
2.937-3.2830.17930.1421739X-RAY DIFFRACTION100
3.283-3.7890.173780.1511550X-RAY DIFFRACTION99.9386
3.789-4.6350.154570.1341336X-RAY DIFFRACTION99.9283
4.635-6.5350.253510.1821040X-RAY DIFFRACTION99.9084
6.535-38.7620.179340.181624X-RAY DIFFRACTION98.7988

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