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- PDB-1m9z: CRYSTAL STRUCTURE OF HUMAN TGF-BETA TYPE II RECEPTOR LIGAND BINDI... -

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Basic information

Entry
Database: PDB / ID: 1m9z
TitleCRYSTAL STRUCTURE OF HUMAN TGF-BETA TYPE II RECEPTOR LIGAND BINDING DOMAIN
ComponentsTGF-BETA RECEPTOR TYPE II
KeywordsHORMONE/GROWTH FACTOR / three finger toxin fold / HORMONE-GROWTH FACTOR COMPLEX
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 / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / activin receptor activity / 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 / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / activin receptor activity / TGFBR2 MSI Frameshift Mutants in Cancer / miRNA transport / transforming growth factor beta ligand-receptor complex / type III transforming growth factor beta receptor binding / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / cardiac left ventricle morphogenesis / secondary palate development / 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 / TGFBR3 regulates TGF-beta signaling / positive regulation of NK T cell differentiation / transforming growth factor beta receptor activity, type I / 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 / transforming growth factor beta receptor activity, type III / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / activin binding / regulation of stem cell proliferation / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / pattern specification process / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / glycosaminoglycan binding / regulation of stem cell differentiation / response to cholesterol / kinase activator activity / embryonic cranial skeleton morphogenesis / transforming growth factor beta binding / aortic valve morphogenesis / lens development in camera-type eye / embryonic hemopoiesis / atrioventricular valve morphogenesis / positive regulation of mesenchymal cell proliferation / artery morphogenesis / trachea formation / smoothened signaling pathway / ventricular septum morphogenesis / branching involved in blood vessel morphogenesis / roof of mouth development / blood vessel development / SMAD binding / heart looping / TGF-beta receptor signaling activates SMADs / outflow tract morphogenesis / positive regulation of epithelial cell migration / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / vasculogenesis / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / gastrulation / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cellular response to growth factor stimulus / brain development / caveola / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / UCH proteinases / heart development / regulation of cell population proliferation / regulation of gene expression / molecular adaptor activity / in utero embryonic development / receptor complex / membrane raft / response to xenobiotic stimulus / external side of plasma membrane / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / extracellular space / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Mainly Beta
Similarity search - Domain/homology
TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.05 Å
AuthorsBoesen, C.C. / Radaev, S. / Motyka, S.A. / Patamawenu, A. / Sun, P.D.
CitationJournal: Structure / Year: 2002
Title: THE 1.1A CRYSTAL STRUCTURE OF HUMAN TGF-BETA TYPE II RECEPTOR LIGAND BINDING DOMAIN
Authors: Boesen, C.C. / Radaev, S. / Motyka, S.A. / Patamawenu, A. / Sun, P.D.
History
DepositionJul 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-BETA RECEPTOR TYPE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7162
Polymers12,6241
Non-polymers921
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.471, 40.658, 76.154
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 II / TGFR-2 / TGF-beta type II receptor


Mass: 12624.248 Da / Num. of mol.: 1 / Fragment: Extracellular / Mutation: Q26A,K97T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P37173
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 2000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: Boesen, C.C., (2002) Acta Crystallogr., D58, 1214.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
230 %PEG20001reservoir
30.1 Msodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0092, 1.0011, 1.0076
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00921
21.00111
31.00761
ReflectionResolution: 1.05→36 Å / Num. all: 45991 / Num. obs: 43635 / % possible obs: 87.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 8 Å2 / Rsym value: 0.035 / Net I/σ(I): 56.5
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 3.9 % / Num. unique all: 2277 / Rsym value: 0.488 / % possible all: 44.3
Reflection
*PLUS
Lowest resolution: 36 Å / Num. obs: 45991 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 44.3 % / Num. unique obs: 2277 / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.05→35.81 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.973 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16615 2306 5 %RANDOM
Rwork0.15595 ---
obs0.15647 43635 87.96 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.05→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 6 178 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021842
X-RAY DIFFRACTIONr_bond_other_d0.0010.02703
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9581139
X-RAY DIFFRACTIONr_angle_other_deg0.68631661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7093104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45915153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_nbd_refined0.2240.3177
X-RAY DIFFRACTIONr_nbd_other0.2080.3749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1430.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.521
X-RAY DIFFRACTIONr_mcbond_it1.0291.5529
X-RAY DIFFRACTIONr_mcangle_it1.6682862
X-RAY DIFFRACTIONr_scbond_it2.2253313
X-RAY DIFFRACTIONr_scangle_it3.2974.5277
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 79
Rwork0.292 1512
Refinement
*PLUS
Lowest resolution: 36 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.166 / Rfactor Rwork: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48
LS refinement shell
*PLUS
Lowest resolution: 1.09 Å / Rfactor Rfree: 0.29

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