9B9F: Zebrafish Betaglycan Orphan Domain

Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII. Determined by X-ray diffraction at 3.0 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Danio rerio
Chains: 10
Atoms: 11,078
Mol. weight: 170.9 kDa
Released: 12 Mar 2025

Explore 9B9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9F contains 35 α-helices and 133 β-strands across 10 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	302-303	2	1
α-helix	304-309	6
β-strand	316-318	3	2
β-strand	321-323	3	3
α-helix	324-327	4
β-strand	335	1	4
β-strand	338-340	3	3
β-strand	343-345	3	2
β-strand	354	1	1
α-helix	357-368	12
α-helix	370-372	3
β-strand	378-380	3	1
β-strand	383-392	10	4
β-strand	395-406	12	4
β-strand	408-411	4	1

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	302-303	2	5
α-helix	304-309	6
β-strand	316-318	3	6
β-strand	321-323	3	7
α-helix	324-328	5
β-strand	333-335	3	8
β-strand	338-340	3	7
β-strand	343-345	3	6
β-strand	354	1	5
α-helix	357-368	12
α-helix	370-372	3
β-strand	378-380	3	5
β-strand	383-392	10	8
β-strand	395-406	12	8
β-strand	408-411	4	5

Chains C and H: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	9
α-helix	40-42	3
β-strand	45-48	4	9
β-strand	51-59	9	10
β-strand	62-70	9	10
α-helix	72-74	3
β-strand	95-99	5	10

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
α-helix	48-49	2
β-strand	50-52	3	4
β-strand	55-58	4	11
β-strand	66-68	3	12
β-strand	74-76	3	4
β-strand	83-91	9	11
β-strand	94-102	9	11
β-strand	108	1	13
β-strand	111	1	13
β-strand	121-122	2	12
β-strand	124-128	5	11
β-strand	131-138	8	11
β-strand	146-148	3	12

Chain E: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	35	1	14
α-helix	36	1
β-strand	42-50	9	8
β-strand	53-56	4	15
α-helix	59-61	3
β-strand	67-72	6	15
β-strand	86-91	6	8
α-helix	103-104	2
β-strand	105-109	5	15
β-strand	115-119	5	8
β-strand	131-133	3	15
β-strand	139-141	3	8
β-strand	152-154	3	15
α-helix	161-171	11
β-strand	177-181	5	15
β-strand	186-189	4	8
β-strand	204	1	15
β-strand	209	1	16
β-strand	212	1	16
β-strand	213-219	7	8
β-strand	223-226	4	14
β-strand	235-243	9	14
β-strand	252-260	9	8
β-strand	267-268	2	17
β-strand	271-277	7	14
β-strand	281-287	7	8
β-strand	290-291	2	17
β-strand	292-298	7	14
β-strand	301-304	4	8
α-helix	306-311	6
β-strand	312-315	4	14
α-helix	326-334	9
β-strand	341-349	9	14
β-strand	352-357	6	8

Chain F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	302-303	2	18
α-helix	304-309	6
β-strand	316-318	3	19
β-strand	321-323	3	20
α-helix	324-328	5
β-strand	335	1	21
β-strand	338-340	3	20
β-strand	343-345	3	19
β-strand	354	1	18
α-helix	357-368	12
α-helix	370-372	3
β-strand	378-380	3	18
β-strand	383-392	10	21
β-strand	395-406	12	21
β-strand	408-411	4	18

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	302-303	2	22
α-helix	304-308	5
β-strand	316-318	3	23
β-strand	321-323	3	24
α-helix	324-328	5
β-strand	333-335	3	25
β-strand	338-340	3	24
β-strand	343-345	3	23
β-strand	354	1	22
α-helix	357-368	12
α-helix	370-372	3
β-strand	378-380	3	22
β-strand	383-392	10	25
β-strand	395-406	12	25
β-strand	408-411	4	22

Chain I: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
α-helix	48-49	2
β-strand	50-52	3	21
β-strand	55-58	4	28
β-strand	66-68	3	29
β-strand	74-76	3	21
β-strand	83-91	9	28
β-strand	94-102	9	28
β-strand	107-108	2	30
β-strand	111-112	2	30
β-strand	121-122	2	29
β-strand	124-128	5	28
β-strand	131-138	8	28
β-strand	146-148	3	29

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-3	A, F	protein	112	Homo sapiens	P10600 (AlphaFold model)
Transforming growth factor beta-3 triple mutant	B, G	protein	112	Homo sapiens	P10600 (AlphaFold model)
Transforming growth factor beta receptor type-1	C, H	protein	87	Homo sapiens	P36897 (AlphaFold model)
Transforming growth factor beta receptor type-2	D, I	protein	113	Homo sapiens	P37173 (AlphaFold model)
Transforming growth factor beta receptor type-3	E, J	protein	338	Danio rerio	E7FDB6 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>9B9F_1 Transforming growth factor beta-3 (chains A, F)
ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS

Sequence of entity 2 (B, G), FASTA

>9B9F_2 Transforming growth factor beta-3 triple mutant (chains B, G)
ALDTNYCFRNLEENCCVRPLYIDFEQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST
VLGLYNTLNPEASASPCCVPQDLEPLTILAYVGETPKVEQLSNMVVKSCKCS

Sequence of entity 3 (C, H), FASTA

>9B9F_3 Transforming growth factor beta receptor type-1 (chains C, H)
GSATALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSMCIAEIDLIPRDRPFVCAP
SSKTGSVTTTYCCNQDHCNKIELPTTV

Sequence of entity 4 (D, I), FASTA

>9B9F_4 Transforming growth factor beta receptor type-2 (chains D, I)
MNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETV
CHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Sequence of entity 5 (E, J), FASTA

>9B9F_5 Transforming growth factor beta receptor type-3 (chains E, J)
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
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
9FK5 4.1 Å, Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular…

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