3KFD: Transforming growth factor beta-1

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily. Determined by X-ray diffraction at 3.0 Å resolution. Released 2 Mar 2010.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,151
Mol. weight: 141.46 kDa
Released: 2 Mar 2010

Explore 3KFD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KFD contains 23 α-helices and 113 β-strands across 12 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.

Chains A and C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	4-7	4
β-strand	16-18	3	2
β-strand	21-23	3	3
α-helix	24-28	5
β-strand	33-35	3	1
β-strand	38-40	3	3
β-strand	43-45	3	2
β-strand	54	1	1
α-helix	57-68	12
β-strand	78-92	15	1
β-strand	95-111	17	1

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	4
α-helix	4-7	4
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 D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	23
α-helix	4-7	4
β-strand	16-18	3	24
β-strand	21-23	3	25
α-helix	24-28	5
β-strand	35	1	23
β-strand	38-40	3	25
β-strand	43-45	3	24
β-strand	54	1	23
α-helix	57-68	12
β-strand	78-92	15	23
β-strand	95-111	17	23

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	27-29	3	1
β-strand	32-35	4	7
β-strand	43-44	2	8
β-strand	51-53	3	1
β-strand	60-67	8	7
β-strand	72-79	8	7
β-strand	84	1	9
β-strand	89	1	9
β-strand	95	1	7
β-strand	98-99	2	8
β-strand	103-105	3	7
β-strand	108-115	8	7
α-helix	120-122	3
β-strand	124-125	2	8

Chain F: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	4
β-strand	32-35	4	10
β-strand	45	1	11
β-strand	51-53	3	4
β-strand	60-67	8	10
β-strand	73-79	7	10
β-strand	84	1	12
β-strand	89	1	12
β-strand	98-99	2	13
β-strand	101-102	2	10
β-strand	105	1	14
β-strand	108	1	14
β-strand	109-115	7	10
α-helix	120-122	3
β-strand	123	1	11
β-strand	124-125	2	13

Chain G: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	20
β-strand	32-35	4	26
β-strand	43-45	3	27
β-strand	51-53	3	20
β-strand	60-67	8	26
β-strand	72-79	8	26
β-strand	84	1	28
β-strand	89	1	28
β-strand	95	1	26
β-strand	98-99	2	27
β-strand	103-105	3	26
β-strand	108-115	8	26
α-helix	120-122	3
β-strand	123-125	3	27

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	23
β-strand	34-35	2	29
β-strand	43-45	3	30
β-strand	51-53	3	23
β-strand	60-67	8	29
β-strand	73-79	7	29
β-strand	98-99	2	30
β-strand	101-102	2	29
β-strand	105	1	31
β-strand	108	1	31
β-strand	109-115	7	29
α-helix	120-122	3
β-strand	123-125	3	30

Chain I: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	15
β-strand	12-13	2	16
α-helix	18-20	3
β-strand	23-24	2	16
β-strand	29-33	5	17
β-strand	45-48	4	17
β-strand	74-75	2	17
β-strand	80	1	15

2 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-1	A, B, C, D	protein	112	Homo sapiens	P01137 (AlphaFold model)
TGF-beta receptor type-2	E, F, G, H	protein	116	Homo sapiens	P37173 (AlphaFold model)
TGF-beta receptor type-1	I, J, K, L	protein	85	Homo sapiens	P36897 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3KFD_1 Transforming growth factor beta-1 (chains A, B, C, D)
ALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSK
VLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Sequence of entity 2 (E, F, G, H), FASTA

>3KFD_2 TGF-beta receptor type-2 (chains E, F, G, H)
VTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITL
ETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY

Sequence of entity 3 (I, J, K, L), FASTA

>3KFD_3 TGF-beta receptor type-1 (chains I, J, K, L)
ATALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSMCIAEIDLIPRDRPFVCAPSS
KTGSVTTTYCCNQDHCNKIELPTTV

Primary citation

Ternary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily. Radaev, S., Zou, Z., Huang, T. et al. J Biol Chem (2010) 285:14806-14814. DOI 10.1074/jbc.M109.079921 · 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…
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
8VSD 3.2 Å, avb8/L-TGF-b1/GARP

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