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- PDB-1ktz: Crystal Structure of the Human TGF-beta Type II Receptor Extracel... -

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Basic information

Entry
Database: PDB / ID: 1ktz
TitleCrystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex with TGF-beta3
Components
  • TGF-beta Type II Receptor
  • TRANSFORMING GROWTH FACTOR BETA 3
KeywordsCYTOKINE/CYTOKINE RECEPTOR / CYTOKINE-RECEPTOR COMPLEX / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / bronchus morphogenesis / mammary gland morphogenesis / detection of hypoxia / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / bronchus morphogenesis / mammary gland morphogenesis / detection of hypoxia / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / frontal suture morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / embryonic neurocranium morphogenesis / miRNA transport / transforming growth factor beta ligand-receptor complex / aorta morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / negative regulation of macrophage cytokine production / 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 / TGFBR3 regulates TGF-beta signaling / lung lobe morphogenesis / positive regulation of tight junction disassembly / positive regulation of NK T cell differentiation / response to laminar fluid shear stress / activin receptor complex / transforming growth factor beta receptor activity, type I / activin receptor activity, type II / BMP receptor activity / type II transforming growth factor beta receptor binding / activin receptor activity, type I / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / transforming growth factor beta receptor activity, type III / activin binding / regulation of stem cell proliferation / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / mammary gland development / outflow tract septum morphogenesis / activin receptor signaling pathway / glycosaminoglycan binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / cell-cell junction organization / regulation of stem cell differentiation / response to cholesterol / embryonic cranial skeleton morphogenesis / transforming growth factor beta binding / kinase activator activity / digestive tract development / aortic valve morphogenesis / face morphogenesis / atrioventricular valve morphogenesis / lens development in camera-type eye / odontogenesis / positive regulation of filopodium assembly / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / artery morphogenesis / Molecules associated with elastic fibres / trachea formation / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / lung alveolus development / blood vessel development / SMAD binding / heart looping / negative regulation of vascular associated smooth muscle cell proliferation / roof of mouth development / inner ear development / outflow tract morphogenesis / TGF-beta receptor signaling activates SMADs / positive regulation of cell division / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / ECM proteoglycans / vasculogenesis / salivary gland morphogenesis / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / Notch signaling pathway / gastrulation / T-tubule / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen
Similarity search - Function
Transforming growth factor beta-3 / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related ...Transforming growth factor beta-3 / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / 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
Transforming growth factor beta-3 proprotein / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsHart, P.J. / Deep, S. / Taylor, A.B. / Shu, Z. / Hinck, C.S. / Hinck, A.P.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex.
Authors: Hart, P.J. / Deep, S. / Taylor, A.B. / Shu, Z. / Hinck, C.S. / Hinck, A.P.
History
DepositionJan 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: TRANSFORMING GROWTH FACTOR BETA 3
B: TGF-beta Type II Receptor


Theoretical massNumber of molelcules
Total (without water)26,5882
Polymers26,5882
Non-polymers00
Water2,936163
1
A: TRANSFORMING GROWTH FACTOR BETA 3
B: TGF-beta Type II Receptor

A: TRANSFORMING GROWTH FACTOR BETA 3
B: TGF-beta Type II Receptor


Theoretical massNumber of molelcules
Total (without water)53,1764
Polymers53,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)114.41, 114.41, 209.43
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe second part of the biological assembly is generated by the crystallographic symmetry operator y, x, -z and a translation of one unit cell length along the z-axis.

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Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA 3 / TGF-beta3


Mass: 12734.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10600
#2: Protein TGF-beta Type II Receptor / TBR-2


Mass: 13853.632 Da / Num. of mol.: 1 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P37173, EC: 2.7.1.37
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 5 Å3/Da / Density % sol: 75 %
Crystal growDetails: HANGING DROP VAPOR DIFFUSION USING A WELL SOLUTION CONTAINING 20% (V/V) 2-METHYL-2,4-PENTANEDIOL AND 0.1 M CITRATE PH 4.0
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 %(v/v)MPD1reservoir
3100 mMcitrate1reservoirpH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→26 Å / Num. all: 29006 / Num. obs: 29006 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.5
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2824 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 154181
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.15→25.61 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3888970.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2002 6.9 %RANDOM
Rwork0.201 ---
obs0.201 28916 99.8 %-
all-29064 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0368 Å2 / ksol: 0.356719 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20.34 Å20 Å2
2---2.25 Å20 Å2
3---4.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-26 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.15→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 0 163 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it3.973
X-RAY DIFFRACTIONc_scangle_it5.384.5
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 200 7.1 %
Rwork0.265 2632 -
obs-2832 98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 26 Å / σ(F): 0 / % reflection Rfree: 6.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_scbond_it3.973
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scangle_it5.384.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 7.1 % / Rfactor Rwork: 0.265

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