9FDY: Betaglycan Orphan Domain

Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII. Determined by electron microscopy at 3.4 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 5
Atoms: 6,119
Mol. weight: 89.58 kDa
Released: 12 Mar 2025

Explore 9FDY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FDY contains 15 α-helices and 70 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
β-strand	16-18	3	1
β-strand	21-23	3	2
α-helix	24-28	5
β-strand	35	1	3
β-strand	38-40	3	2
β-strand	43-45	3	1
β-strand	54	1	3
α-helix	57-68	12
β-strand	78-92	15	3
β-strand	95-111	17	3

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	4
α-helix	4-9	6
β-strand	16-18	3	5
β-strand	21-23	3	6
α-helix	24-28	5
β-strand	35	1	4
β-strand	38-40	3	6
β-strand	43-45	3	5
β-strand	54	1	4
α-helix	57-68	12
β-strand	78-92	15	4
β-strand	95-111	17	4

Chain C: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	7
β-strand	15-23	9	8
β-strand	26-29	4	9
β-strand	39-46	8	9
β-strand	58-59	2	10
β-strand	60-65	6	8
β-strand	72	1	11
β-strand	76-81	6	9
β-strand	87-88	2	10
β-strand	91-92	2	8
β-strand	95	1	11
β-strand	101-106	6	9
β-strand	110-111	2	10
α-helix	113-114	2
α-helix	118-121	4
β-strand	122-127	6	9
α-helix	133-144	12
β-strand	149-154	6	9
β-strand	158-163	6	8
β-strand	176	1	9
β-strand	185-192	8	8
β-strand	195-198	4	7
β-strand	206-215	10	7
β-strand	229-234	6	8
β-strand	241-251	11	7
β-strand	256-261	6	8
β-strand	264-271	8	7
β-strand	275-278	4	8
α-helix	281-283	3
β-strand	284	1	8
β-strand	287-291	5	7
α-helix	300-310	11
β-strand	317-323	7	7
β-strand	326-331	6	8

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	3
β-strand	17-20	4	12
β-strand	29-31	3	13
β-strand	37-39	3	3
β-strand	46-51	6	12
β-strand	60-65	6	12
β-strand	71	1	14
β-strand	74	1	14
α-helix	77-80	4
β-strand	85	1	13
β-strand	87-89	3	12
β-strand	96-101	6	12
β-strand	109-111	3	13

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13-15	3	4
β-strand	20-21	2	15
β-strand	29-31	3	16
β-strand	37-39	3	4
β-strand	46-53	8	15
β-strand	58-65	8	15
α-helix	70	1
β-strand	71	1	17
β-strand	74	1	17
β-strand	85	1	16
β-strand	87-89	3	15
β-strand	95-101	7	15
α-helix	106-108	3
β-strand	109-111	3	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1	A, B	protein	112	Homo sapiens	P01137 (AlphaFold model)
Transforming growth factor beta receptor type 3	C	protein	339	Rattus norvegicus	P26342 (AlphaFold model)
TGF-beta receptor type-2	D, E	protein	113	Homo sapiens	P37173 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9FDY_1 Transforming growth factor beta-1 (chains A, B)
ALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSK
VLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Sequence of entity 2 (C), FASTA

>9FDY_2 Transforming growth factor beta receptor type 3 (chains C)
GSPCELSPINASHPVQALMESFTVLSGCASRGTTGLPREVHVLNLRSTDQGPGQRQREVT
LHLNPIASVHTHHKPIVFLLNSPQPLVWHLKTERLAAGVPRLFLVSEGSVVQFPSGNFSL
TAETEERNFPQENEHLLRWAQKEYGAVTSFTELKIARNIYIKVGEDQVFPPTCNIGKNFL
SLNYLAEYLQPKAAEGCVLPSQPHEKEVHIIELITPSSNPYSAFQVDIIVDIRPAQEDPE
VVKNLVLILKCKKSVNWVIKSFDVKGNLKVIAPNSIGFGKESERSMTMTKLVRDDIPSTQ
ENLMKWALDNGYRPVTSYTMAPVANRFHLRLENHHHHHH

Sequence of entity 3 (D, E), FASTA

>9FDY_3 TGF-beta receptor type-2 (chains D, E)
MNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETV
CHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Primary citation

Structures of TGF-beta with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling. Wieteska, L., Taylor, A.B., Punch, E. et al. Nat Commun (2025) 16:1778-1778. DOI 10.1038/s41467-025-56796-9 · PubMed

Other PDB entries of the same protein (UniProt P01137 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UDZ 2.21 Å, The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex
9VJJ 2.48 Å, Crystal Structure of human Latent TGF-beta1 in complex with SOF10
8C7H 2.7 Å, Cryo-EM Map of the latTGF-beta LHG-10 Fab complex
13FJ 2.75 Å, TGFB1 in complex with NIS793 FAB
6OM2 2.77 Å, Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
5VQP 2.9 Å, Crystal structure of human pro-TGF-beta1
8REW 2.98 Å, CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an…
3KFD 3.0 Å, Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor…
4KV5 3.0 Å, scFv GC1009 in complex with TGF-beta1.
8VSC 3.0 Å, L-tgf-b1/GARP
9R3S 3.06 Å, pro-TGF-beta1 in complex with the third TB Domain from Latent Transforming Growth…
6GFF 3.1 Å, Structure of GARP (LRRC32) in complex with latent TGF-beta1 and MHG-8 Fab

Browse structure collections

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