9FKP: Zebrafish Betaglycan Orphan Domain

Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-b1 and extracellular domain of TGFBRII. Determined by electron microscopy at 3.72 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.72 Å
Organisms: Homo sapiens, Danio rerio
Chains: 5
Atoms: 6,092
Mol. weight: 89.2 kDa
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9FKP contains 16 α-helices and 66 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, 9 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
α-helix	57-68	12
β-strand	78-80	3	4
β-strand	83-92	10	3
β-strand	95-106	12	3
β-strand	109-111	3	4

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
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	7
β-strand	38-40	3	6
β-strand	43-45	3	5
α-helix	57-68	12
β-strand	78-92	15	7
β-strand	95-111	17	7

Chain C: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	13
α-helix	36-37	2
β-strand	42-50	9	7
β-strand	53-56	4	14
α-helix	59-61	3
β-strand	66-73	8	14
α-helix	84-85	2
β-strand	86-93	8	7
β-strand	100	1	15
β-strand	104-108	5	14
β-strand	115-120	6	7
β-strand	123	1	15
β-strand	130-133	4	14
β-strand	138-141	4	7
α-helix	144-149	6
β-strand	151-154	4	14
α-helix	161-172	12
β-strand	177-182	6	14
β-strand	187-191	5	7
β-strand	204	1	14
β-strand	209	1	7
β-strand	212-219	8	7
β-strand	223-225	3	13
β-strand	235-243	9	13
β-strand	252-260	9	7
β-strand	267-268	2	16
β-strand	271-277	7	13
β-strand	281-287	7	7
β-strand	290-291	2	16
β-strand	292-298	7	13
β-strand	302-304	3	7
α-helix	306-311	6
β-strand	312-314	3	13
α-helix	326-335	10
β-strand	343-349	7	13
β-strand	352-357	6	7

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	8
β-strand	57	1	9
β-strand	66-67	2	10
β-strand	74	1	8
β-strand	75-76	2	3
α-helix	82	1
β-strand	83-88	6	9
β-strand	97-102	6	9
β-strand	122	1	10
β-strand	124-126	3	9
β-strand	133-138	6	9
β-strand	147-148	2	10

Chain E: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	50-52	3	7
β-strand	57-58	2	11
β-strand	67-68	2	12
β-strand	74-76	3	7
α-helix	77	1
β-strand	83-90	8	11
β-strand	95-102	8	11
β-strand	122-126	5	11
β-strand	132-138	7	11
α-helix	143-145	3
β-strand	146-147	2	12
β-strand	148	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1	A, B	protein	112	Homo sapiens	P01137 (AlphaFold model)
TGF-beta receptor type-2	D, E	protein	113	Homo sapiens	P37173 (AlphaFold model)
Transforming growth factor beta receptor III	C	protein	338	Danio rerio	E7FDB6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9FKP_1 Transforming growth factor beta-1 (chains A, B)
ALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSK
VLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Sequence of entity 2 (D, E), FASTA

>9FKP_2 TGF-beta receptor type-2 (chains D, E)
MNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETV
CHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Sequence of entity 3 (C), FASTA

>9FKP_3 Transforming growth factor beta receptor III (chains C)
GSPCELLPVGVGHPVQAMLKSFTALSGCASRGTTSHPQEVHIINLRKGSAQGAREKTAEV
ALHLRPIQSLHVHQKPLVFILNSPQPILWKVRTEKLAPGVKRIFHVVEGSEVHFEVGNFS
KSGEVKVETLPHGNEHLLNWAHHRYTAVTSFSELRMAHDIYIKVGEDPVFSETCKIDNKF
LSLNYLASYIEPQPSTGCVLSGPDHEQEVHIIELQAPNSSSAFQVDVIVDLRPLDGDIPL
HRDVVLLLKGEKSVNWVIKAHKVMGKLEIMTSDTVSLSEDTERLMQVSKTVKQKLPAGSQ
ALIQWAEENGFNPVTSYTNTPVANHFNLRLREHHHHHH

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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