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- EMDB-50326: Betaglycan in complex with TGF-b1 -

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Basic information

Entry
Database: EMDB / ID: EMD-50326
TitleBetaglycan in complex with TGF-b1
Map dataSharpened map
Sample
  • Complex: Complex of Betaglycan and TGF-b1
    • Complex: Betaglycan
      • Protein or peptide: Betaglycan
    • Complex: TGF-b1 homodimer
      • Protein or peptide: TGF-b1
      • Protein or peptide: TGF-b1
KeywordsComplex / Betaglycan / TGF-b1 / Cytokine / MEMBRANE PROTEIN
Function / homology
Function and homology information


TGFBR3 PTM regulation / TGFBR3 regulates FGF2 signaling / negative regulation of apoptotic process involved in morphogenesis / TGFBR3 regulates activin signaling / response to luteinizing hormone / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / transforming growth factor beta receptor complex assembly / epicardium-derived cardiac fibroblast cell development ...TGFBR3 PTM regulation / TGFBR3 regulates FGF2 signaling / negative regulation of apoptotic process involved in morphogenesis / TGFBR3 regulates activin signaling / response to luteinizing hormone / FGFR1b ligand binding and activation / FGFR1c ligand binding and activation / TGF-beta receptor signaling activates SMADs / transforming growth factor beta receptor complex assembly / epicardium-derived cardiac fibroblast cell development / Signaling by BMP / inhibin-betaglycan-ActRII complex / muscular septum morphogenesis / definitive erythrocyte differentiation / cellular response to acetaldehyde / 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 / Influenza Virus Induced Apoptosis / response to follicle-stimulating hormone / TGFBR3 regulates TGF-beta signaling / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis / macrophage derived foam cell differentiation / frontal suture morphogenesis / regulation of enamel mineralization / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulatory T cell differentiation / tolerance induction to self antigen / regulation of blood vessel remodeling / regulation of protein import into nucleus / BMP binding / embryonic liver development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / vasculogenesis involved in coronary vascular morphogenesis / columnar/cuboidal epithelial cell maturation / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / apoptotic process involved in morphogenesis / myofibroblast differentiation / odontoblast differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / Signaling by Activin / negative regulation of macrophage cytokine production / positive regulation of smooth muscle cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of exit from mitosis / ventricular compact myocardium morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / secondary palate development / negative regulation of epithelial cell migration / 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 / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / heart valve morphogenesis / retina vasculature development in camera-type eye / TGFBR3 regulates TGF-beta signaling / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / cardiac epithelial to mesenchymal transition / positive regulation of vasculature development / response to laminar fluid shear stress / collagen metabolic process / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / negative regulation of extracellular matrix disassembly / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / receptor catabolic process / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / transforming growth factor beta receptor activity, type III / activin binding / heart trabecula morphogenesis / oligodendrocyte development / type I transforming growth factor beta receptor binding / response to salt / germ cell migration / negative regulation of biomineral tissue development / positive regulation of mononuclear cell migration / endoderm development / phospholipid homeostasis / negative regulation of myoblast differentiation / positive regulation of chemotaxis / negative regulation of cell-cell adhesion mediated by cadherin / glycosaminoglycan binding
Similarity search - Function
Transforming growth factor beta-1 proprotein / : / : / : / ZP-N domain / Transforming growth factor-beta / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain ...Transforming growth factor beta-1 proprotein / : / : / : / 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 / 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 cytokine
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein / Transforming growth factor beta receptor type 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.39 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)GM058067 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
DepositionMay 16, 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_50326.png

Downloads & links

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Map

FileDownload / File: emd_50326.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.333774 - 0.4346769
Average (Standard dev.)0.00031327433 (±0.019711502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50326_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_50326_additional_1.map
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Half map: #1

Fileemd_50326_half_map_1.map
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Half map: #2

Fileemd_50326_half_map_2.map
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Sample components

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Entire : Complex of Betaglycan and TGF-b1

EntireName: Complex of Betaglycan and TGF-b1
Components
  • Complex: Complex of Betaglycan and TGF-b1
    • Complex: Betaglycan
      • Protein or peptide: Betaglycan
    • Complex: TGF-b1 homodimer
      • Protein or peptide: TGF-b1
      • Protein or peptide: TGF-b1

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Supramolecule #1: Complex of Betaglycan and TGF-b1

SupramoleculeName: Complex of Betaglycan and TGF-b1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 25 KDa

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Supramolecule #2: Betaglycan

SupramoleculeName: Betaglycan / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: TGF-b1 homodimer

SupramoleculeName: TGF-b1 homodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TGF-b1

MacromoleculeName: TGF-b1 / type: protein_or_peptide / ID: 1 / Details: Homodimer / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALDTNYCFSS TEKNCCVRQL YIDFRKDLGW KWIHEPKGYH ANFCLGPCPY IWSLDTQYSK VLALYNQHNP GASAAPCCVP QALEPLPIVY YVGRKPKVEQ LSNMIVRSCK CS

UniProtKB: Transforming growth factor beta-1 proprotein

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Macromolecule #2: TGF-b1

MacromoleculeName: TGF-b1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALDTNYCFSS TEKNCCVRQL YIDFRKDLGW KWIHEPKGYH ANFCLGPCPY IWSLDTQYSK VLALYNQHNP GASAAPCCVP QALEPLPIVY YVGRKPKVEQ LSNMIVRSCK CS

UniProtKB: Transforming growth factor beta-1 proprotein

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Macromolecule #3: Betaglycan

MacromoleculeName: Betaglycan / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVTSHHMIP VMVVLMSACL ATAGPEPSTR CELSPINASH PVQALMESFT VLSGCASRGT TGLPREVHVL NLRSTDQGPG QRQREVTLHL NPIASVHTHH KPIVFLLNSP QPLVWHLKTE RLAAGVPRLF LVSEGSVVQF PSGNFSLTAE TEERNFPQEN EHLLRWAQKE ...String:
MAVTSHHMIP VMVVLMSACL ATAGPEPSTR CELSPINASH PVQALMESFT VLSGCASRGT TGLPREVHVL NLRSTDQGPG QRQREVTLHL NPIASVHTHH KPIVFLLNSP QPLVWHLKTE RLAAGVPRLF LVSEGSVVQF PSGNFSLTAE TEERNFPQEN EHLLRWAQKE YGAVTSFTEL KIARNIYIKV GEDQVFPPTC NIGKNFLSLN YLAEYLQPKA AEGCVLPSQP HEKEVHIIEL ITPSSNPYSA FQVDIIVDIR PAQEDPEVVK NLVLILKCKK SVNWVIKSFD VKGNLKVIAP NSIGFGKESE RSMTMTKLVR DDIPSTQENL MKWALDNGYR PVTSYTMAPV ANRFHLRLEN NEEMRDEEVH TIPPELRILL DPDHPPALDN PLFPGEGSPN GGLPFPFPDI PRRGWKEGED RIPRPKQPIV PSVQLLPDHR EPEEVQGGVD IALSVKCDHE KMVVAVDKDS FQTNGYSGME LTLLDPSCKA KMNGTHFVLE SPLNGCGTRH RRSTPDGVVY YNSIVVQAPS PGDSSGWPDG YEDLESGDNG FPGDGDEGET APLSRAGVVV FNCSLRQLRN PSGFQGQLDG NATFNMELYN TDLFLVPSPG VFSVAENEHV YVEVSVTKAD QDLGFAIQTC FLSPYSNPDR MSDYTIIENI CPKDDSVKFY SSKRVHFPIP HAEVDKKRFS FLFKSVFNTS LLFLHCELTL CSRKKGSLKL PRCVTPDDAC TSLDATMIWT MMQNKKTFTK PLAVVLQVDY KENVPSTKDS SPIPPPPPQI FHGLDTLTVM GIAFAAFVIG ALLTGALWYI YSHTGETARR QQVPTSPPAS ENSSAAHSIG STQSTPCSSS STA

UniProtKB: Transforming growth factor beta receptor type 3

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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

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 258006
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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