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- EMDB-50519: Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3... -

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Entry
Database: EMDB / ID: EMD-50519
TitleZebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
Map data
Sample
  • Complex: Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
    • Complex: Zebrafish Betaglycan - Orphan domain
      • Protein or peptide: Transforming growth factor beta receptor III
    • Complex: complex part - TGF-B3 and extracellular domains of TGFBRI and TGFBRII
      • Protein or peptide: Transforming growth factor beta-3
      • Protein or peptide: Transforming growth factor beta-3
      • Protein or peptide: TGF-beta receptor type-1
      • Protein or peptide: TGF-beta receptor type-2
KeywordsComplex / Betaglycan / TGFBR3 / TGFb / TGFBR1 / TGFBR2 / MEMBRANE PROTEIN
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 / uterine wall breakdown / inferior endocardial cushion 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 / 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 / extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / TGFBR2 MSI Frameshift Mutants in Cancer / embryonic neurocranium morphogenesis / miRNA transport / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / type III transforming growth factor beta receptor binding / aorta morphogenesis / myofibroblast differentiation / 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 / ventricular compact myocardium morphogenesis / cardiac left ventricle morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / secondary palate development / trophoblast cell migration / positive regulation of mesenchymal stem cell proliferation / 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 / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of vasculature development / response to laminar fluid shear stress / somite development / neuron fate commitment / activin receptor complex / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / 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 / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / pharyngeal system development / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / transforming growth factor beta receptor activity, type III / activin binding / regulation of epithelial to mesenchymal transition / regulation of stem cell proliferation / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / germ cell migration / filopodium assembly / mammary gland development / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / glycosaminoglycan binding / cell-cell junction organization / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of stem cell differentiation / response to cholesterol / embryonic cranial skeleton morphogenesis / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / kinase activator activity / digestive tract development / aortic valve morphogenesis / negative regulation of chondrocyte differentiation / sprouting angiogenesis / face morphogenesis / atrioventricular valve morphogenesis / endothelial cell activation / anterior/posterior pattern specification
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 / : / : / ZP-N domain / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. ...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 / : / : / ZP-N domain / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Activin types I and II receptor domain / 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. / Protein kinase domain / 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-3 proprotein / TGF-beta receptor type-1 / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Danio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWieteska L / Coleman JA / Hinck AP
Funding support United States, European Union, 2 items
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 2, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50519.png

Downloads & links

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Map

FileDownload / File: emd_50519.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193
Minimum - Maximum-0.61481357 - 1.3156903
Average (Standard dev.)-0.00013211218 (±0.016207779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_50519_additional_1.map
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Additional map: #1

Fileemd_50519_additional_2.map
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Half map: #2

Fileemd_50519_half_map_1.map
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Half map: #1

Fileemd_50519_half_map_2.map
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Sample components

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Entire : Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in ...

EntireName: Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
Components
  • Complex: Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
    • Complex: Zebrafish Betaglycan - Orphan domain
      • Protein or peptide: Transforming growth factor beta receptor III
    • Complex: complex part - TGF-B3 and extracellular domains of TGFBRI and TGFBRII
      • Protein or peptide: Transforming growth factor beta-3
      • Protein or peptide: Transforming growth factor beta-3
      • Protein or peptide: TGF-beta receptor type-1
      • Protein or peptide: TGF-beta receptor type-2

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Supramolecule #1: Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in ...

SupramoleculeName: Quinary complex of Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90 KDa

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Supramolecule #2: Zebrafish Betaglycan - Orphan domain

SupramoleculeName: Zebrafish Betaglycan - Orphan domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Danio rerio (zebrafish)

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Supramolecule #3: complex part - TGF-B3 and extracellular domains of TGFBRI and TGFBRII

SupramoleculeName: complex part - TGF-B3 and extracellular domains of TGFBRI and TGFBRII
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transforming growth factor beta-3

MacromoleculeName: Transforming growth factor beta-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.734504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCSGPCPY LRSADTTHST VLGLYNTLNP EASASPCCVP QDLEPLTIL YYVGRTPKVE QLSNMVVKSC KCS

UniProtKB: Transforming growth factor beta-3 proprotein

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Macromolecule #2: Transforming growth factor beta-3

MacromoleculeName: Transforming growth factor beta-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.586247 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALDTNYCFRN LEENCCVRPL YIDFEQDLGW KWVHEPKGYY ANFCSGPCPY LRSADTTHST VLGLYNTLNP EASASPCCVP QDLEPLTIL AYVGETPKVE QLSNMVVKSC KCS

UniProtKB: Transforming growth factor beta-3 proprotein

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Macromolecule #3: TGF-beta receptor type-1

MacromoleculeName: TGF-beta receptor type-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein serine/threonine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.474826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSATALQCFC HLCTKDNFTC VTDGLCFVSV TETTDKVIHN SMCIAEIDLI PRDRPFVCAP SSKTGSVTTT YCCNQDHCNK IELPTTV

UniProtKB: TGF-beta receptor type-1

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Macromolecule #4: TGF-beta receptor type-2

MacromoleculeName: TGF-beta receptor type-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein serine/threonine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.926812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNGAVKFPQL CKFCDVRFST CDNQKSCMSN CSITSICEKP QEVCVAVWRK NDENITLETV CHDPKLPYHD FILEDAASPK CIMKEKKKP GETFFMCSCS SDECNDNIIF SEEY

UniProtKB: TGF-beta receptor type-2

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Macromolecule #5: Transforming growth factor beta receptor III

MacromoleculeName: Transforming growth factor beta receptor III / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 37.727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSPCELLPVG VGHPVQAMLK SFTALSGCAS RGTTSHPQEV HIINLRKGSA QGAREKTAEV ALHLRPIQSL HVHQKPLVFI LNSPQPILW KVRTEKLAPG VKRIFHVVEG SEVHFEVGNF SKSGEVKVET LPHGNEHLLN WAHHRYTAVT SFSELRMAHD I YIKVGEDP ...String:
GSPCELLPVG VGHPVQAMLK SFTALSGCAS RGTTSHPQEV HIINLRKGSA QGAREKTAEV ALHLRPIQSL HVHQKPLVFI LNSPQPILW KVRTEKLAPG VKRIFHVVEG SEVHFEVGNF SKSGEVKVET LPHGNEHLLN WAHHRYTAVT SFSELRMAHD I YIKVGEDP VFSETCKIDN KFLSLNYLAS YIEPQPSTGC VLSGPDHEQE VHIIELQAPN SSSAFQVDVI VDLRPLDGDI PL HRDVVLL LKGEKSVNWV IKAHKVMGKL EIMTSDTVSL SEDTERLMQV SKTVKQKLPA GSQALIQWAE ENGFNPVTSY TNT PVANHF NLRLREHHHH HH

UniProtKB: Transforming growth factor beta receptor III

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9b9f

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 281881
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9b9f


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9fk5:
Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII

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