8VSC: L-tgf-b1/GARP

L-tgf-b1/GARP. Determined by electron microscopy at 3.0 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,844
Mol. weight: 154.85 kDa
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8VSC contains 38 α-helices and 70 β-strands across 3 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: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-27	19
α-helix	33-35	3
α-helix	39-40	2
α-helix	44-45	2
α-helix	46-56	11
β-strand	77-83	7	1
α-helix	84-86	3
α-helix	87-91	5
β-strand	101-107	7	2
α-helix	108-114	7
α-helix	118-120	3
β-strand	121-130	10	1
β-strand	137-144	8	2
β-strand	152-158	7	2
β-strand	165-170	6	1
α-helix	172-181	10
β-strand	185-192	8	2
β-strand	207	1	1
β-strand	228-233	6	1
α-helix	236-239	4
β-strand	265-268	4	3
β-strand	271	1	4
α-helix	273-277	5
β-strand	282-284	3	5
β-strand	288	1	4
β-strand	291-294	4	3
β-strand	327-341	15	5
β-strand	344-360	17	5

Chain B: 15 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3	1	6
α-helix	4	1
α-helix	9-27	19
α-helix	33-35	3
α-helix	40-41	2
α-helix	43-45	3
α-helix	46-56	11
β-strand	77-83	7	5
α-helix	84-86	3
α-helix	87-91	5
α-helix	92-95	4
β-strand	101-107	7	7
α-helix	108-114	7
β-strand	121-130	10	5
β-strand	137-144	8	7
β-strand	150-158	9	7
β-strand	165-170	6	5
α-helix	172-181	10
β-strand	185-192	8	7
β-strand	207	1	5
β-strand	228-233	6	5
α-helix	236-238	3
β-strand	265-267	3	8
β-strand	271-272	2	9
β-strand	282-284	3	1
β-strand	287-288	2	9
β-strand	292-294	3	8
α-helix	298-302	5
α-helix	314-317	4
β-strand	327-341	15	1
β-strand	344-360	17	1

Chain I: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	10
β-strand	32-34	3	10
β-strand	53-55	3	10
β-strand	63-64	2	11
α-helix	66-69	4
β-strand	77-79	3	10
β-strand	87-88	2	11
α-helix	92-95	4
β-strand	101-103	3	10
α-helix	109-111	3
β-strand	128-130	3	10
β-strand	137	1	12
α-helix	141-144	4
β-strand	153-155	3	10
β-strand	160	1	12
β-strand	163-164	2	13
β-strand	177-179	3	10
β-strand	187-188	2	13
β-strand	201-203	3	10
β-strand	211-212	2	6
β-strand	222-224	3	10
β-strand	232-233	2	6
β-strand	247-249	3	10
β-strand	269-271	3	10
β-strand	319-321	3	10
α-helix	332-337	6
β-strand	343-345	3	10
β-strand	353-354	2	14
β-strand	367-369	3	10
β-strand	377-378	2	14
α-helix	380-381	2
β-strand	390-392	3	10
β-strand	414-416	3	10
β-strand	424	1	15
β-strand	437	1	15
β-strand	447-449	3	10
β-strand	457-458	2	16
β-strand	470-472	3	10
β-strand	480-481	2	16
α-helix	487-489	3
β-strand	495-497	3	10
α-helix	510-512	3
β-strand	518-520	3	10
β-strand	540-542	3	10
α-helix	553-556	4
α-helix	559-561	3
β-strand	565-567	3	10
α-helix	580-584	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1 proprotein	A, B	protein	390	Homo sapiens	P01137 (AlphaFold model)
Transforming growth factor beta activator LRRC32	I	protein	608	Homo sapiens	Q14392 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VSC_1 Transforming growth factor beta-1 proprotein (chains A, B)
MPPSGLRLLLLLLPLLWLLVLTPGRPAAGLSTCKTIDMELVKRKRIEAIRGQILSKLRLA
SPPSQGEVPPGPLPEAVLALYNSTRDRVAGESAEPEPEPEADYYAKEVTRVLMVETHNEI
YDKFKQSTHSIYMFFNTSELREAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSNNSWR
YLSNRLLAPSDSPEWLSFDVTGVVRQWLSRGGEIEGFRLSAHCSCDSRDNTLQVDINGFT
TGRRGDLATIHGMNRPFLLLMATPLERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYI
DFRKDLGWKWIHEPKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQA
LEPLPIVYYVGRKPKVEQLSNMIVRSCKCS

Sequence of entity 2 (I), FASTA

>8VSC_2 Transforming growth factor beta activator LRRC32 (chains I)
HQDKVPCKMVDKKVSCQVLGLLQVPSVLPPDTETLDLSGNQLRSILASPLGFYTALRHLD
LSTNEISFLQPGAFQALTHLEHLSLAHNRLAMATALSAGGLGPLPRVTSLDLSGNSLYSG
LLERLLGEAPSLHTLSLAENSLTRLTRHTFRDMPALEQLDLHSNVLMDIEDGAFEGLPRL
THLNLSRNSLTCISDFSLQQLRVLDLSCNSIEAFQTASQPQAEFQLTWLDLRENKLLHFP
DLAALPRLIYLNLSNNLIRLPTGPPQDSKGIHAPSEGWSALPLSAPSGNASGRPLSQLLN
LDLSYNEIELIPDSFLEHLTSLCFLNLSRNCLRTFEARRLGSLPCLMLLDLSHNALETLE
LGARALGSLRTLLLQGNALRDLPPYTFANLASLQRLNLQGNRVSPCGGPDEPGPSGCVAF
SGITSLRSLSLVDNEIELLRAGAFLHTPLTELDLSSNPGLEVATGALGGLEASLEVLALQ
GNGLMVLQVDLPCFICLKRLNLAENRLSHLPAWTQAVSLEVLDLRNNSFSLLPGSAMGGL
ETSLRRLYLQGNPLSCCGNGWLAAQLHQGRVDVDATQDLICRFSSQEEVSLSHVRPEDCE
KGGLKNIN

Primary citation

Dynamic allostery drives autocrine and paracrine TGF-beta signaling. Jin, M., Seed, R.I., Cai, G. et al. Cell (2024) 187:6200. DOI 10.1016/j.cell.2024.08.036 · 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…
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.
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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