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- PDB-8g4k: Complex of TbRII mini protein binder bound to the TbRII ECD -

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Basic information

Entry
Database: PDB / ID: 8g4k
TitleComplex of TbRII mini protein binder bound to the TbRII ECD
Components
  • 5HCS_TGFBR2_1
  • TGF-beta receptor type-2
KeywordsSIGNALING PROTEIN / TbRII / TGF-b type II receptor / Computationally designed mini protein binder / MPB
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 / 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 / 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 / TGFBR3 regulates TGF-beta signaling / membranous septum morphogenesis / positive regulation of NK T cell differentiation / activin receptor complex / activin receptor activity, type I / lung lobe morphogenesis / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / SMAD protein signal transduction / type I transforming growth factor beta receptor binding / myeloid dendritic cell differentiation / embryonic cranial skeleton morphogenesis / activin receptor signaling pathway / glycosaminoglycan binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of stem cell differentiation / outflow tract septum morphogenesis / response to cholesterol / transforming growth factor beta binding / kinase activator activity / aortic valve morphogenesis / lens development in camera-type eye / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / artery morphogenesis / trachea formation / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / blood vessel development / SMAD binding / heart looping / TGF-beta receptor signaling activates SMADs / outflow tract morphogenesis / roof of mouth development / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / vasculogenesis / Downregulation of TGF-beta receptor signaling / gastrulation / Notch signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / transforming growth factor beta receptor signaling pathway / brain development / caveola / cellular response to growth factor stimulus / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / UCH proteinases / nervous system development / regulation of cell population proliferation / regulation of gene expression / heart development / molecular adaptor activity / in utero embryonic development / receptor complex / nuclear body / membrane raft / response to xenobiotic stimulus / external side of plasma membrane / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / extracellular space / extracellular region / ATP binding / metal ion binding / membrane / 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 / 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 ...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 / 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
Similarity search - Domain/homology
TGF-beta receptor type-2
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsSchwartze, T.S. / Hinck, A.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA233622 United States
CitationJournal: To be Published
Title: Computational Design of High Affinity Binders to Convex Protein Target Sites
Authors: Yang, W. / Hicks, D.R. / Scwartze, T.A. / Ghosh, A. / Conventry, B. / Goreshnik, I. / Allen, A. / Halabiya, S.F. / Kim, C.J. / Hinck, C.S. / Lee, D.S. / Bera, A.K. / Li, Z. / Wang, Y. / ...Authors: Yang, W. / Hicks, D.R. / Scwartze, T.A. / Ghosh, A. / Conventry, B. / Goreshnik, I. / Allen, A. / Halabiya, S.F. / Kim, C.J. / Hinck, C.S. / Lee, D.S. / Bera, A.K. / Li, Z. / Wang, Y. / Schlichthaerle, T. / Cao, L. / Huang, B. / Garrett, S. / Gerben, S.R. / Rettie, S. / Heine, P. / Murray, A. / Edman, N. / Carter, L. / Stewart, L. / Almo, S. / Hinck, A.P. / Baker, D.
History
DepositionFeb 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5HCS_TGFBR2_1
B: TGF-beta receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3603
Polymers24,2642
Non-polymers961
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC was performed and showed 1:1 complex, surface plasmon resonance, Related method, bilayer inferometry (BL1) was used to detect low nano molar affinity of 5HCS_TGFBR2_1 for TbRII
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-20 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.983, 57.175, 78.798
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 5HCS_TGFBR2_1


Mass: 11463.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: 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: 12800.656 Da / Num. of mol.: 1 / Fragment: ECD (UNP residues 46-155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37173
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.3 %
Description: Crystals tend to form two dimensional plates, which do diffract; however, in glycerol three-dimensional crystals appeared and produced higher quality diffraction data. Crystals require ...Description: Crystals tend to form two dimensional plates, which do diffract; however, in glycerol three-dimensional crystals appeared and produced higher quality diffraction data. Crystals require at least 0.2 M ammonium sulfate for growth beyond needle clusters.
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% PEG5000 MME, 0.2-0.4 M ammonium sulfate, 0.1 M Tris, pH 7.4, 16-32% glycerol
Temp details: Room Temperature (Uncontrolled)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→78.8 Å / Num. obs: 61539 / % possible obs: 95.7 % / Redundancy: 8.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Χ2: 0.9 / Net I/σ(I): 18.9
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2727 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.662 / Χ2: 0.53 / % possible all: 53.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1m9z

1m9z


Resolution: 1.24→46.28 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1958 3078 5 %
Rwork0.1813 --
obs-61539 99.9 %
Refinement stepCycle: LAST / Resolution: 1.24→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 5 201 1877

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