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- PDB-8ygz: The Crystal Structure of TGF beta R2 kinase domain from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8ygz
TitleThe Crystal Structure of TGF beta R2 kinase domain from Biortus.
ComponentsTGF-beta receptor type-2
KeywordsTRANSFERASE / Serine/threonine-protein kinase / apoptosis / ATP-binding
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 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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 ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of TGF beta R2 kinase domain from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
History
DepositionFeb 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,31412
Polymers35,5871
Non-polymers72711
Water3,171176
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)61.090, 75.020, 77.704
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-2 / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TGF-beta ...TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TGF-beta receptor type II / TbetaR-II


Mass: 35587.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P37173, receptor protein serine/threonine kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 30% PEG4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18064 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18064 Å / Relative weight: 1
ReflectionResolution: 2.1→48.03 Å / Num. obs: 21483 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1719 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.026 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.207 / ESU R Free: 0.191
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.254 1025 4.783 %
Rwork0.1949 20407 -
all0.198 --
obs-21432 99.944 %
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: 44.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.145 Å20 Å20 Å2
2--0.344 Å2-0 Å2
3----1.488 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 47 176 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152291
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6473240
X-RAY DIFFRACTIONr_angle_other_deg1.2631.5785294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48222.602123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73515416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8921514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_nbd_refined0.2040.2524
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22173
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21142
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.211
X-RAY DIFFRACTIONr_nbd_other0.1670.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.27
X-RAY DIFFRACTIONr_mcbond_it3.5284.4021162
X-RAY DIFFRACTIONr_mcbond_other3.5224.3991161
X-RAY DIFFRACTIONr_mcangle_it4.9826.5751447
X-RAY DIFFRACTIONr_mcangle_other4.9816.5781448
X-RAY DIFFRACTIONr_scbond_it3.9984.8471246
X-RAY DIFFRACTIONr_scbond_other3.9974.8491247
X-RAY DIFFRACTIONr_scangle_it5.9437.0641790
X-RAY DIFFRACTIONr_scangle_other5.9427.0661791
X-RAY DIFFRACTIONr_lrange_it7.67951.2542750
X-RAY DIFFRACTIONr_lrange_other7.66750.9552711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.315660.2721490X-RAY DIFFRACTION100
2.154-2.2130.334840.2561424X-RAY DIFFRACTION100
2.213-2.2770.34550.2461408X-RAY DIFFRACTION99.7273
2.277-2.3470.319680.2341393X-RAY DIFFRACTION100
2.347-2.4240.331720.231312X-RAY DIFFRACTION99.9278
2.424-2.5090.349670.2071274X-RAY DIFFRACTION100
2.509-2.6040.255720.2071238X-RAY DIFFRACTION100
2.604-2.710.304620.1941189X-RAY DIFFRACTION100
2.71-2.830.268660.211146X-RAY DIFFRACTION99.9176
2.83-2.9680.286590.2071094X-RAY DIFFRACTION100
2.968-3.1280.229560.1941054X-RAY DIFFRACTION100
3.128-3.3170.243450.1991002X-RAY DIFFRACTION100
3.317-3.5450.214400.192962X-RAY DIFFRACTION99.9003
3.545-3.8270.216480.174876X-RAY DIFFRACTION100
3.827-4.190.166370.156813X-RAY DIFFRACTION100
4.19-4.6820.281360.153758X-RAY DIFFRACTION100
4.682-5.3990.282270.177669X-RAY DIFFRACTION100
5.399-6.5960.218320.215566X-RAY DIFFRACTION100
6.596-9.2590.193180.199455X-RAY DIFFRACTION99.789
9.259-48.030.282150.214284X-RAY DIFFRACTION98.6799

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