7RCO: Human TGF-beta-2

Crystal structure of human TGF-beta-2 bound to 4A11.V2 Fab. Determined by X-ray diffraction at 2.9 Å resolution. Released 29 Sept 2021.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,200
Mol. weight: 121.38 kDa
Released: 29 Sept 2021

Explore 7RCO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RCO contains 30 α-helices and 109 β-strands across 6 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	304-305	2	1
α-helix	306-311	6
β-strand	316	1	2
β-strand	318-320	3	3
β-strand	323-325	3	4
α-helix	326-330	5
β-strand	340-342	3	4
β-strand	345-347	3	3
β-strand	349	1	2
α-helix	359-370	12
β-strand	376	1	5
α-helix	377-378	2
β-strand	380-382	3	1
β-strand	385-389	5	6
β-strand	392	1	7
β-strand	399	1	7
β-strand	402-408	7	6
β-strand	410-413	4	1

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	305	1	8
α-helix	306-309	4
β-strand	316	1	9
β-strand	318-320	3	10
β-strand	323-325	3	11
α-helix	326-330	5
β-strand	337	1	8
β-strand	340-342	3	11
β-strand	345-347	3	10
β-strand	349	1	9
α-helix	359-370	12
β-strand	380-394	15	8
β-strand	397-413	17	8

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	13
α-helix	45-46	2
β-strand	47-51	5	13
β-strand	55-56	2	13
β-strand	64-69	6	12
β-strand	72-77	6	12
α-helix	82-84	3
β-strand	86-93	8	13
β-strand	101-103	3	13
β-strand	108-112	5	13
β-strand	116	1	14
β-strand	119-123	5	15
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	15
β-strand	145	1	14
β-strand	149-155	7	16
β-strand	158-159	2	16
α-helix	160	1
β-strand	164-168	5	15
α-helix	169-172	4
β-strand	178-187	10	15
α-helix	188-192	5
β-strand	196-203	8	16
β-strand	210-215	6	16

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	10-12	3	18
β-strand	18-25	8	17
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	57-59	3	18
α-helix	61-63	3
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-98	8	18
β-strand	112-115	4	18
β-strand	119-123	5	18
β-strand	129	1	19
α-helix	130-131	2
β-strand	132-136	5	20
β-strand	148-157	10	20
β-strand	158	1	19
β-strand	163-166	4	21
α-helix	167-169	3
β-strand	175-177	3	20
α-helix	178-180	3
β-strand	181-182	2	20
β-strand	188-196	9	20
α-helix	200-203	4
β-strand	204	1	22
β-strand	207-212	6	21
α-helix	213-215	3
β-strand	217-222	6	21

Chain E: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-14	5	24
β-strand	19-25	7	23
α-helix	28-29	2
α-helix	30-32	3
β-strand	35-40	6	24
α-helix	45-46	2
β-strand	47-51	5	24
β-strand	55-56	2	24
β-strand	64-69	6	23
β-strand	72-77	6	23
α-helix	82-84	3
β-strand	86-93	8	24
β-strand	101-103	3	24
β-strand	107-112	6	24
β-strand	116	1	25
β-strand	119-123	5	26
α-helix	124-126	3
β-strand	137-142	6	26
β-strand	145	1	25
β-strand	150-155	6	27
β-strand	166-168	3	26
β-strand	179-184	6	26
α-helix	188-191	4
β-strand	197-202	6	27

Chain F: 1 helix, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	11-12	2	29
β-strand	17-24	8	28
β-strand	34-39	6	30
β-strand	45-51	7	30
β-strand	55	1	5
β-strand	57-59	3	30
β-strand	67-72	6	28
β-strand	77-83	7	28
β-strand	91-98	8	30
β-strand	112-115	4	30
β-strand	119-121	3	30
β-strand	122-123	2	29
β-strand	132-136	5	31
β-strand	148-157	10	31
β-strand	162-166	5	32
β-strand	176-177	2	31
α-helix	178-180	3
β-strand	181	1	31
β-strand	188-196	9	31
β-strand	201	1	33
β-strand	204	1	33
β-strand	207-212	6	32
β-strand	221-222	2	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-2	A, B	protein	112	Homo sapiens	P61812 (AlphaFold model)
4A11.V2 Fab Light Chain	C, E	protein	219	Homo sapiens
4A11.V2 Fab Heavy Chain	D, F	protein	233	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7RCO_1 Transforming growth factor beta-2 (chains A, B)
ALDAAYCFRNVQDNCCLRPLYIDFKRDLGWKWIHEPKGYNANFCAGACPYLWSSDTQHSR
VLSLYNTINPEASASPCCVSQDLEPLTILYYIGKTPKIEQLSNMIVKSCKCS

Sequence of entity 2 (C, E), FASTA

>7RCO_2 4A11.V2 Fab Light Chain (chains C, E)
DAQLTQSPSSLSASVGDRVTITCQSSQSVYNNNYLSWFQQKPGKPPKLLIYGASTLTSGV
PSRFSGSGSGTDFTLTISSLQPEDFATYYCAGGYSGSSDKYAFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, F), FASTA

>7RCO_3 4A11.V2 Fab Heavy Chain (chains D, F)
EQQLVESGGGLVQPGGSLRLSCAVSGFSLSSYTVNWVRQAPGKGLEWIGYISYGGSAYYA
SWANGRFTISKDSAKNSVYLQMNSLRAEDTAVYFCARHMQVGGAPTGSMAAFDPWGPGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Primary citation

Dramatic activation of an antibody by a single amino acid change in framework. Liang, W.C., Yin, J., Lupardus, P. et al. Sci Rep (2021) 11:22365-22365. DOI 10.1038/s41598-021-01530-w · 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…
8FXS 3.15 Å, Crystal structure of human pro-TGF-beta2 in complex with Nb9

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