7Y1R: Human L-TGF-beta1

Human L-TGF-beta1 in complex with the anchor protein LRRC33. Determined by electron microscopy at 4.01 Å resolution. Released 31 Aug 2022.

Method: Electron microscopy
Resolution: 4.01 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,565
Mol. weight: 162.21 kDa
Ligands: NAG
Released: 31 Aug 2022

Explore 7Y1R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y1R contains 28 α-helices and 63 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
β-strand	2	1	1
α-helix	16-28	13
α-helix	43-45	3
α-helix	46-56	11
β-strand	77-78	2	2
β-strand	80-82	3	3
α-helix	83-85	3
α-helix	90-94	5
β-strand	101	1	4
α-helix	108-114	7
β-strand	123-126	4	3
β-strand	138-143	6	5
β-strand	151-157	7	5
α-helix	171-173	3
β-strand	190	1	4
β-strand	229-232	4	3
α-helix	253-258	6
β-strand	265-267	3	6
β-strand	271-272	2	7
β-strand	284	1	8
β-strand	287-288	2	7
β-strand	292-294	3	6
α-helix	297-299	3
α-helix	300-303	4
α-helix	308-311	4
α-helix	319-322	4
β-strand	327-338	12	8
β-strand	347-360	14	8

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5-27	23
α-helix	32-34	3
α-helix	43-45	3
α-helix	46-56	11
α-helix	58-59	2
β-strand	78-81	4	8
α-helix	91-94	4
β-strand	102	1	9
β-strand	105-107	3	10
α-helix	108-114	7
β-strand	123-129	7	8
β-strand	142-143	2	11
β-strand	151-152	2	11
β-strand	166-170	5	8
α-helix	172-180	9
β-strand	185-187	3	10
β-strand	188-189	2	11
β-strand	190	1	9
α-helix	226-228	3
β-strand	229-233	5	8
α-helix	236-238	3
β-strand	265-267	3	12
β-strand	271-272	2	13
β-strand	284	1	2
β-strand	287-288	2	13
β-strand	292-294	3	12
α-helix	300-302	3
α-helix	309-317	9
β-strand	328-329	2	14
β-strand	332-341	10	2
β-strand	344-355	12	2
β-strand	358-359	2	14

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	37-38	2
β-strand	46-47	2	15
β-strand	53	1	16
β-strand	70-71	2	15
β-strand	77	1	16
α-helix	82-85	4
β-strand	93-94	2	15
β-strand	119-121	3	15
α-helix	128-134	7
β-strand	144-145	2	15
β-strand	153-154	2	17
β-strand	168-169	2	15
β-strand	177-178	2	17
β-strand	189-192	4	18
β-strand	201-202	2	19
β-strand	204	1	1
β-strand	210-213	4	18
β-strand	216	1	20
β-strand	222-223	2	19
β-strand	236-238	3	18
β-strand	240	1	20
β-strand	258-260	3	18
α-helix	327-331	5
β-strand	349-350	2	21
β-strand	364-366	3	22
β-strand	373-374	2	21
β-strand	388-392	5	22
β-strand	412-415	4	22
β-strand	448-450	3	22
β-strand	471-473	3	22
β-strand	497-499	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-1 proprotein	A, B	protein	377	Homo sapiens	P01137 (AlphaFold model)
Transforming growth factor beta activator LRRC33	E	protein	656	Homo sapiens	Q86YC3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7Y1R_1 Transforming growth factor beta-1 proprotein (chains A, B)
MPLLLLLPLLWAGALALSTCKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGEVPPGPL
PEAVLALYNSTRDRVAGESAEPEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYM
FFNTSELREAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSP
EWLSFDVTGVVRQWLSRGGEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGM
NRPFLLLMATPLERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHE
PKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRK
PKVEQLSNMIVRSCKCS

Sequence of entity 2 (E), FASTA

>7Y1R_2 Transforming growth factor beta activator LRRC33 (chains E)
MPLLLLLPLLWAGALAWRNRSGTATAASQGVCKLVGGAADCRGQSLASVPSSLPPHARML
TLDANPLKTLWNHSLQPYPLLESLSLHSCHLERISRGAFQEQGHLRSLVLGDNCLSENYE
ETAAALHALPGLRRLDLSGNALTEDMAALMLQNLSSLRSVSLAGNTIMRLDDSVFEGLER
LRELDLQRNYIFEIEGGAFDGLAELRHLNLAFNNLPCIVDFGLTRLRVLNVSYNVLEWFL
ATGGEAAFELETLDLSHNQLLFFPLLPQYSKLRTLLLRDNNMGFYRDLYNTSSPREMVAQ
FLLVDGNVTNITTVSLWEEFSSSDLADLRFLDMSQNQFQYLPDGFLRKMPSLSHLNLHQN
CLMTLHIREHEPPGALTELDLSHNQLSELHLAPGLASCLGSLRLFNLSSNQLLGVPPGLF
ANARNITTLDMSHNQISLCPLPAASDRVGPPSCVDFRNMASLRSLSLEGCGLGALPDCPF
QGTSLTYLDLSSNWGVLNGSLAPLQDVAPMLQVLSLRNMGLHSSFMALDFSGFGNLRDLD
LSGNCLTTFPRFGGSLALETLDLRRNSLTALPQKAVSEQLSRGLRTIYLSQNPYDCCGVD
GWGALQHGQTVADWAMVTCNLSSKIIRVTELPGGVPRDCKWERLDLGSNSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Specificity of TGF-beta 1 signal designated by LRRC33 and integrin alpha V beta 8. Duan, Z., Lin, X., Wang, L. et al. Nat Commun (2022) 13:4988-4988. DOI 10.1038/s41467-022-32655-9 · 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.
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

Browse structure collections

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