8UDZ: LTBP-49247 Fab

The Structure of LTBP-49247 Fab Bound to TGFbeta1 Small Latent Complex. Determined by X-ray diffraction at 2.21 Å resolution. Released 17 Jul 2024.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,329
Mol. weight: 180.97 kDa
Ligands: NAG
Released: 17 Jul 2024

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

Secondary structure: helices and β-sheets

8UDZ contains 48 α-helices and 126 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	38-56	19
α-helix	62-64	3
α-helix	68-70	3
α-helix	75-85	11
β-strand	106-112	7	1
β-strand	114	1	2
β-strand	131-136	6	2
α-helix	137-143	7
α-helix	147-149	3
β-strand	150-157	8	1
β-strand	166-170	5	2
β-strand	184-187	4	2
α-helix	188-189	2
β-strand	196-199	4	1
α-helix	201-207	7
β-strand	214-221	8	2
β-strand	224-227	4	3
β-strand	232-235	4	3
β-strand	257-262	6	1
β-strand	284	1	4
β-strand	294-296	3	4
β-strand	299-301	3	5
α-helix	302-306	5
β-strand	311	1	6
β-strand	316-318	3	5
β-strand	321-323	3	4
β-strand	356-370	15	6
β-strand	373-389	17	6

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	38-56	19
α-helix	72-74	3
α-helix	75-85	11
β-strand	106-112	7	6
α-helix	113-115	3
β-strand	130-136	7	7
α-helix	137-143	7
α-helix	147-149	3
β-strand	150-159	10	6
β-strand	162	1	8
β-strand	166-173	8	7
β-strand	179-187	9	7
β-strand	190	1	8
β-strand	194-199	6	6
α-helix	201-207	7
β-strand	214-221	8	7
β-strand	225	1	9
β-strand	234	1	9
β-strand	248	1	6
β-strand	257-262	6	6
β-strand	294-296	3	10
β-strand	299-301	3	11
α-helix	302-306	5
β-strand	311-313	3	1
β-strand	316-318	3	11
β-strand	321-323	3	10
β-strand	356-370	15	1
β-strand	373-389	17	1

Chain C: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
α-helix	103-106	4
β-strand	108-111	4	13
β-strand	115-119	5	13
α-helix	126-127	2
β-strand	128-135	8	14
β-strand	145-153	9	14
β-strand	158-162	5	15
α-helix	163-165	3
β-strand	171-178	8	14
β-strand	184-191	8	14
β-strand	202-208	7	15
β-strand	217-219	3	15

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	16
β-strand	9-11	3	17
β-strand	18-24	7	16
α-helix	29-31	3
β-strand	35-39	5	17
β-strand	46-49	4	17
β-strand	50	1	18
β-strand	54	1	18
β-strand	63-68	6	16
β-strand	73-78	6	16
α-helix	83-85	3
β-strand	87-95	9	17
β-strand	100-103	4	17
β-strand	107-110	4	17
β-strand	117	1	19
α-helix	118-119	2
β-strand	120-124	5	20
α-helix	125-127	3
α-helix	128-131	4
β-strand	136-145	10	20
β-strand	146	1	19
β-strand	151-156	6	21
β-strand	159-161	3	21
β-strand	165-167	3	20
α-helix	168-170	3
β-strand	171-172	2	20
β-strand	178-186	9	20
α-helix	188-193	6
β-strand	197-203	7	21
β-strand	206-212	7	21

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	19-25	7	22
α-helix	29-31	3
β-strand	34-39	6	24
β-strand	45-52	8	24
β-strand	55-60	6	24
α-helix	62-64	3
β-strand	69-73	5	22
α-helix	74-76	3
β-strand	78-82	5	22
β-strand	92-99	8	24
α-helix	103-106	4
β-strand	108-111	4	24
β-strand	115-117	3	24
β-strand	118-119	2	23
β-strand	125	1	25
α-helix	126-127	2
β-strand	128-138	11	26
β-strand	143-153	11	26
β-strand	154	1	25
β-strand	159-162	4	27
α-helix	163-165	3
β-strand	171-173	3	26
α-helix	174-176	3
β-strand	177-178	2	26
β-strand	184-193	10	26
α-helix	194-196	3
β-strand	203-208	6	27
α-helix	209-211	3
β-strand	213-218	6	27

Chain F: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	28
β-strand	9-12	4	29
β-strand	18-24	7	28
α-helix	29-31	3
β-strand	35-39	5	29
α-helix	44-45	2
β-strand	46-49	4	29
β-strand	50	1	30
β-strand	54	1	30
α-helix	55-56	2
β-strand	63-68	6	28
α-helix	69-71	3
β-strand	73-78	6	28
α-helix	83-85	3
β-strand	87-94	8	29
β-strand	101-103	3	29
β-strand	104	1	28
β-strand	107-111	5	29
β-strand	117	1	31
α-helix	118-119	2
β-strand	120-124	5	32
α-helix	125-127	3
α-helix	128-132	5
β-strand	136-145	10	32
β-strand	146	1	31
β-strand	151-156	6	33
β-strand	159-161	3	33
β-strand	165-167	3	32
α-helix	168-170	3
β-strand	171-172	2	32
β-strand	178-186	9	32
α-helix	188-193	6
β-strand	197-203	7	33
β-strand	206-212	7	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1 proprotein	A, B	protein	361	Homo sapiens	P01137 (AlphaFold model)
LTBP-49247 Fab Heavy Chain	C, E	protein	233	Homo sapiens
LTBP-49247 Fab Light Chain	D, F	protein	218	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8UDZ_1 Transforming growth factor beta-1 proprotein (chains A, B)
LSTSKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVA
GESAEPEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVL
LSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLS
RGGEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGMNRPFLLLMATPLERAQ
HLQSSRHRAALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYI
WSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKC
S

Sequence of entity 2 (C, E), FASTA

>8UDZ_2 LTBP-49247 Fab Heavy Chain (chains C, E)
QVQLVESGGGVVQPGRSLRLSCAASGFTFRSYVMHWVRQAPGKGLEWVAVISHEGSLKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARPRIAARRGGFGYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH

Sequence of entity 3 (D, F), FASTA

>8UDZ_3 LTBP-49247 Fab Light Chain (chains D, F)
NFMLTQPHSVSESPGKTVTISCTRSSGNIDNNYVQWYQQRPGSSPTTVIYEDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDYDTQGVVFGGGTKLTVLGQPKAAPS
VTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAA
SSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

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

Primary citation

An antibody that inhibits TGF-beta 1 release from latent extracellular matrix complexes attenuates the progression of renal fibrosis. Jackson, J.W., Streich Jr., F.C., Pal, A. et al. Sci Signal (2024) 17:eadn6052-eadn6052. DOI 10.1126/scisignal.adn6052 · PubMed

Other PDB entries of the same protein (UniProt P01137 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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…
3KFD 3.0 Å, Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor…
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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