9FK5: Zebrafish Betaglycan Orphan Domain

Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII. Determined by electron microscopy at 4.1 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 4.1 Å
Organisms: Homo sapiens, Danio rerio
Chains: 5
Atoms: 5,765
Mol. weight: 85.45 kDa
Released: 12 Mar 2025

Explore 9FK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FK5 contains 14 α-helices and 67 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	304-309	6
β-strand	316-318	3	1
β-strand	322-323	2	2
β-strand	335	1	3
β-strand	338-339	2	2
β-strand	343-345	3	1
β-strand	354	1	4
α-helix	357-368	12
α-helix	370-372	3
β-strand	378-380	3	4
β-strand	383-392	10	3
β-strand	395-406	12	3
β-strand	409-411	3	4

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	304-309	6
β-strand	316-318	3	5
β-strand	321-323	3	6
α-helix	324-328	5
β-strand	333-335	3	7
β-strand	338-340	3	6
β-strand	343-345	3	5
β-strand	354	1	7
α-helix	357-368	12
β-strand	378-392	15	7
β-strand	395-411	17	7

Chain C: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	8
β-strand	46-48	3	8
β-strand	51-58	8	9
β-strand	63-70	8	9
β-strand	93-99	7	9

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	50-52	3	3
β-strand	57-58	2	10
β-strand	66-68	3	11
β-strand	74-76	3	3
β-strand	83-91	9	10
β-strand	94-102	9	10
β-strand	121-122	2	11
β-strand	124-125	2	10
β-strand	128	1	12
β-strand	131	1	12
β-strand	132-138	7	10
α-helix	143-145	3
β-strand	146-148	3	11

Chain E: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	13
β-strand	42-49	8	7
β-strand	53-56	4	14
α-helix	59-61	3
β-strand	66-71	6	14
α-helix	84-85	2
β-strand	86-87	2	15
β-strand	90-91	2	16
β-strand	100	1	17
β-strand	104-109	6	14
β-strand	115-116	2	15
β-strand	117	1	18
β-strand	119	1	16
β-strand	123	1	17
β-strand	130-133	4	14
β-strand	140	1	18
α-helix	144-148	5
β-strand	151-154	4	14
α-helix	161-172	12
β-strand	177-180	4	14
β-strand	188-189	2	16
β-strand	204	1	14
β-strand	209	1	16
β-strand	212-213	2	16
β-strand	215-220	6	7
β-strand	223-224	2	13
β-strand	226	1	13
β-strand	234-243	10	13
β-strand	252-260	9	7
β-strand	268-277	10	13
β-strand	281-287	7	7
β-strand	291-298	8	13
β-strand	302-304	3	7
α-helix	306-311	6
β-strand	312-314	3	13
α-helix	315-317	3
α-helix	326-334	9
β-strand	343-349	7	13
β-strand	352-357	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-3	A	protein	112	Homo sapiens	P10600 (AlphaFold model)
Transforming growth factor beta-3	B	protein	112	Homo sapiens	P10600 (AlphaFold model)
TGF-beta receptor type-1	C	protein	87	Homo sapiens	P36897 (AlphaFold model)
TGF-beta receptor type-2	D	protein	113	Homo sapiens	P37173 (AlphaFold model)
Transforming growth factor beta receptor III	E	protein	338	Danio rerio	E7FDB6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9FK5_1 Transforming growth factor beta-3 (chains A)
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS

Sequence of entity 2 (B), FASTA

>9FK5_2 Transforming growth factor beta-3 (chains B)
ALDTNYCFRNLEENCCVRPLYIDFEQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILAYVGETPKVEQLSNMVVKSCKCS

Sequence of entity 3 (C), FASTA

>9FK5_3 TGF-beta receptor type-1 (chains C)
GSATALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSMCIAEIDLIPRDRPFVCAP
SSKTGSVTTTYCCNQDHCNKIELPTTV

Sequence of entity 4 (D), FASTA

>9FK5_4 TGF-beta receptor type-2 (chains D)
MNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETV
CHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Sequence of entity 5 (E), FASTA

>9FK5_5 Transforming growth factor beta receptor III (chains E)
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 P10600 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TGJ 2.0 Å, Human transforming growth factor-beta 3, crystallized from dioxane
1KTZ 2.15 Å, Crystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex…
4UM9 2.5 Å, Crystal structure of alpha V beta 6 with peptide
8V52 2.5 Å, Crystal structure of 2A10 Fab bound to Human TGF-beta3
8VS6 2.73 Å, L-TGF-b3/avb8
8VSB 2.93 Å, L-tgf-b3/GARP
2PJY 3.0 Å, Structural basis for cooperative assembly of the TGF-beta signaling complex
9B9F 3.0 Å, Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular…
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
1TGK 3.3 Å, Human transforming growth factor beta 3, crystallized from peg 4000

Browse structure collections

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