8FXS: Human pro-TGF-beta2

Crystal structure of human pro-TGF-beta2 in complex with Nb9. Determined by X-ray diffraction at 3.15 Å resolution. Released 21 Jun 2023.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 6,710
Mol. weight: 118.44 kDa
Ligands: NAG
Released: 21 Jun 2023

Explore 8FXS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FXS contains 19 α-helices and 64 β-strands across 4 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	30-48	19
α-helix	65-81	17
β-strand	101-107	7	1
α-helix	108-111	4
β-strand	121-124	4	2
β-strand	127-130	4	2
α-helix	135-143	9
β-strand	144-153	10	1
β-strand	163-171	9	2
β-strand	182-191	10	2
α-helix	195-196	2
β-strand	197-202	6	1
α-helix	204-212	9
α-helix	214-216	3
β-strand	220-224	5	2
β-strand	250	1	1
β-strand	280-285	6	1
α-helix	288-290	3
β-strand	312	1	3
β-strand	314-316	3	4
β-strand	319-321	3	5
α-helix	322-326	5
β-strand	331-333	3	6
β-strand	336-338	3	5
β-strand	341-343	3	4
β-strand	345	1	3
β-strand	376-378	3	7
β-strand	381-390	10	6
β-strand	393-404	12	6
β-strand	407-409	3	7

Chain B: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	33-48	16
α-helix	65-82	18
β-strand	101-107	7	6
α-helix	108-111	4
β-strand	121-122	2	8
β-strand	123	1	9
β-strand	127-130	4	8
α-helix	135-143	9
β-strand	144-153	10	6
β-strand	164-171	8	8
β-strand	182-190	9	8
α-helix	195-196	2
β-strand	197-202	6	6
α-helix	204-212	9
α-helix	214-216	3
β-strand	220-224	5	8
α-helix	225	1
β-strand	250	1	6
β-strand	280-285	6	6
α-helix	288-290	3
β-strand	314-316	3	10
β-strand	319-321	3	11
α-helix	322-326	5
β-strand	331-333	3	1
β-strand	336-338	3	11
β-strand	341-343	3	10
β-strand	376-378	3	12
β-strand	381-390	10	1
β-strand	393-404	12	1
β-strand	407-409	3	12

Chain D: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	11-12	2	14
β-strand	17-23	7	13
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	56-59	4	2
β-strand	67-72	6	13
β-strand	77-83	7	13
β-strand	91-97	7	2
β-strand	108	1	2
β-strand	112-114	3	2
β-strand	115-116	2	14

Chain E: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	11-12	2	16
β-strand	18-24	7	15
β-strand	34-39	6	9
β-strand	45-52	8	9
β-strand	56-59	4	9
β-strand	67-72	6	15
β-strand	77-82	6	15
β-strand	91-96	6	9
β-strand	112-114	3	9
β-strand	115-116	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-2 proprotein	A, B	protein	393	Homo sapiens	P61812 (AlphaFold model)
Nanobody clone 9	D, E	protein	124	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8FXS_1 Transforming growth factor beta-2 proprotein (chains A, B)
GPSLSTSSTLDMDQFMRKRIEAIRGQILSKLKLTSPPEDYPEPEEVPPEVISIYNSTRDL
LQEKASRRAAACERERSDEEYYAKEVYKIDMPPFFPSENAIPPTFYRPYFRIVRFDVSAM
EKRASNLVKAEFRVFRLQNPKARVPEQRIELYQILKSKDLTSPTQRYIDSKVVKTRAEGE
WLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVPSNNYIIPNKSEELEARFAGIDGTS
TYTSGDQKTIKSTRKKNSGKTPHLLLMLLPSYRLESQQTNGALDAAYCFRNVQDNCCLRP
LYIDFKRDLGWKWIHEPKGYNANFCAGACPYLWSSDTQHSRVLSLYNTINPEASASPCCV
SQDLEPLTILYYIGKTPKIEQLSNMIVKSCKCS

Sequence of entity 2 (D, E), FASTA

>8FXS_2 Nanobody clone 9 (chains D, E)
QVQLQESGGGLVQAGGSLRLSCAASGTIFEANIMGWYRQAPGKERELVAGIGYGSSTYYA
DSVKSRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAQNRDGWYFYYWGQGTQVTVSSHH
HHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

A specialized integrin-binding motif enables proTGF-beta 2 activation by integrin alpha V beta 6 but not alpha V beta 8. Le, V.Q., Zhao, B., Ramesh, S. et al. Proc Natl Acad Sci U S A (2023) 120:e2304874120-e2304874120. DOI 10.1073/pnas.2304874120 · PubMed

Other PDB entries of the same protein (UniProt P61812 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2TGI 1.8 Å, Crystal structure of transforming growth factor-BETA2: an unusual fold for the superfamily
5TX4 1.88 Å, Derivative of mouse TGF-beta2, with a deletion of residues 52-71 and K25R, R26K, L51R,…
6XM2 1.91 Å, The structure of the 4A11.v7 antibody in complex with human TGFb2
8DC0 1.93 Å, Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2…
1TFG 1.95 Å, An unusual feature revealed by the crystal structure at 2.2 Å resolution of human…
6I9J 2.0 Å, Human transforming growth factor beta2 in a tetragonal crystal form
8FXV 2.2 Å, Crystal structure of human proTGF-beta2 in complex with Nb18
4KXZ 2.83 Å, crystal structure of tgfb2 in complex with GC2008.
5TY4 2.9 Å, MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A…
7RCO 2.9 Å, Crystal structure of human TGF-beta-2 bound to 4A11.V2 Fab

Browse structure collections

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