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- PDB-9fkp: Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-b1... -

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Basic information

Entry
Database: PDB / ID: 9fkp
TitleZebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-b1 and extracellular domain of TGFBRII
Components
  • TGF-beta receptor type-2
  • Transforming growth factor beta receptor III
  • Transforming growth factor beta-1
KeywordsMEMBRANE PROTEIN / Complex / Betaglycan / TGFBR3 / TGFb / TGFBR1 / TGFBR2
Function / homology
Function and homology information


FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / bronchus morphogenesis ...FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / TGFBR3 PTM regulation / TGFBR3 regulates TGF-beta signaling / TGFBR3 regulates FGF2 signaling / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / bronchus morphogenesis / cellular response to acetaldehyde / frontal suture morphogenesis / mammary gland morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / lens fiber cell apoptotic process / columnar/cuboidal epithelial cell maturation / transforming growth factor beta receptor activity, type II / growth plate cartilage chondrocyte growth / negative regulation of skeletal muscle tissue development / embryonic liver development / regulation of branching involved in mammary gland duct morphogenesis / tricuspid valve morphogenesis / macrophage derived foam cell differentiation / response to laminar fluid shear stress / regulation of enamel mineralization / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulatory T cell differentiation / regulation of blood vessel remodeling / miRNA transport / tolerance induction to self antigen / regulation of protein import into nucleus / transforming growth factor beta ligand-receptor complex / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / aorta morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / odontoblast differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / positive regulation of exit from mitosis / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of macrophage cytokine production / secondary palate development / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / membrane protein intracellular domain proteolysis / positive regulation of T cell tolerance induction / positive regulation of receptor signaling pathway via STAT / retina vasculature development in camera-type eye / heart valve morphogenesis / positive regulation of extracellular matrix assembly / TGFBR3 regulates TGF-beta signaling / membranous septum morphogenesis / mammary gland branching involved in thelarche / bronchiole development / positive regulation of NK T cell differentiation / hyaluronan catabolic process / lung lobe morphogenesis / somite development / positive regulation of vasculature development / activin receptor complex / lens fiber cell differentiation / activin receptor activity, type I / negative regulation of extracellular matrix disassembly / ATP biosynthetic process / type II transforming growth factor beta receptor binding / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / positive regulation of branching involved in ureteric bud morphogenesis / receptor catabolic process / TGFBR1 LBD Mutants in Cancer / activin binding / regulation of stem cell proliferation / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / negative regulation of biomineral tissue development / germ cell migration / positive regulation of mononuclear cell migration / phospholipid homeostasis / response to salt
Similarity search - Function
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-1 proprotein / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain ...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-1 proprotein / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / 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. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / 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
Transforming growth factor beta receptor III / Transforming growth factor beta-1 proprotein / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsWieteska, L. / Coleman, J.A. / Hinck, A.P.
Funding support United States, European Union, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM058670 United States
H2020 Marie Curie Actions of the European Commission893196European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structures of TGF-β with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling.
Authors: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando ...Authors: Łukasz Wieteska / Alexander B Taylor / Emma Punch / Jonathan A Coleman / Isabella O Conway / Yeu-Farn Lin / Chang-Hyeock Byeon / Cynthia S Hinck / Troy Krzysiak / Rieko Ishima / Fernando López-Casillas / Peter Cherepanov / Daniel J Bernard / Caroline S Hill / Andrew P Hinck /
Abstract: Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility ...Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.
History
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
D: TGF-beta receptor type-2
E: TGF-beta receptor type-2
C: Transforming growth factor beta receptor III


Theoretical massNumber of molelcules
Total (without water)89,2005
Polymers89,2005
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Transforming growth factor beta-1 / TGF-beta-1


Mass: 12809.812 Da / Num. of mol.: 2 / Fragment: Mature
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01137
#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: 12926.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P37173, receptor protein serine/threonine kinase
#3: Protein Transforming growth factor beta receptor III / Transforming growth factor beta receptor type 3 precursor


Mass: 37727.000 Da / Num. of mol.: 1 / Mutation: C150G,C277G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: tgfbr3, si:ch73-18k18.1 / Production host: Homo sapiens (human) / References: UniProt: A0A0H3UK16
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B1 and extracellular domains of TGFBRIICOMPLEXall0MULTIPLE SOURCES
2Zebrafish Betaglycan - Orphan domainCOMPLEX#31RECOMBINANT
3complex part - TGF-B1 and extracellular domains TGFBRIICOMPLEX#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.09 MDaYES
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Danio rerio (zebrafish)7955
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Homo sapiens (human)9606
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraX1.7model fitting
9PHENIX1.21model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 307870 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 9B9F

9b9f


Accession code: 9B9F / Source name: PDB / Type: experimental model

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