8VSD: Avb8/L-TGF-b1/GARP

avb8/L-TGF-b1/GARP. Determined by electron microscopy at 3.2 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 16,276
Mol. weight: 252.49 kDa
Ligands: MG, CA, NAG
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8VSD contains 64 α-helices and 146 β-strands across 5 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: 10 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	9
β-strand	23-26	4	10
β-strand	35-40	6	10
β-strand	55-60	6	10
β-strand	67-69	3	10
β-strand	79-81	3	11
β-strand	84-85	2	11
β-strand	87-88	2	12
β-strand	97-100	4	13
β-strand	104-109	6	13
β-strand	113-114	2	12
β-strand	123-124	2	12
β-strand	127-132	6	13
β-strand	135-139	5	13
β-strand	160-164	5	14
β-strand	168-173	6	14
α-helix	176-179	4
β-strand	181	1	15
β-strand	182-186	5	14
α-helix	188-191	4
β-strand	208-209	2	14
α-helix	215-217	3
β-strand	222	1	15
β-strand	225-229	5	16
β-strand	238-243	6	16
α-helix	246-249	4
β-strand	252-256	5	16
β-strand	263-268	6	16
β-strand	279-283	5	17
β-strand	292-297	6	17
β-strand	301-303	3	18
β-strand	309-311	3	18
β-strand	313	1	19
β-strand	314-320	7	17
β-strand	326-329	4	17
β-strand	332	1	17
β-strand	340	1	19
β-strand	343-348	6	20
β-strand	357-362	6	20
α-helix	367-369	3
β-strand	372-378	7	20
β-strand	383-392	10	20
β-strand	407-410	4	9
β-strand	422-426	5	9
α-helix	427-429	3
β-strand	431-437	7	9
α-helix	438-439	2
β-strand	440-441	2	21
β-strand	444	1	22
α-helix	462-463	2
β-strand	473-474	2	23
β-strand	477	1	24
β-strand	480	1	22
β-strand	481	1	25
β-strand	490-491	2	26
β-strand	495	1	27
β-strand	511-512	2	28
α-helix	514-516	3
β-strand	523	1	27
β-strand	527-528	2	26
β-strand	529	1	25
β-strand	536	1	24
β-strand	539-540	2	23
β-strand	541-542	2	28
α-helix	558-560	3
β-strand	577-578	2	21

Chain B: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	76-77	2	29
β-strand	80-85	6	30
β-strand	90-91	2	29
β-strand	94-97	4	29
β-strand	105-112	8	31
α-helix	118-121	4
α-helix	122-124	3
α-helix	129-134	6
β-strand	142-149	8	31
α-helix	170-172	3
α-helix	176-179	4
β-strand	183-189	7	31
α-helix	192-200	9
β-strand	212	1	32
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	31
α-helix	245	1
β-strand	246	1	32
α-helix	247	1
α-helix	250-255	6
α-helix	259-261	3
β-strand	267	1	33
β-strand	271	1	31
β-strand	272	1	33
α-helix	273-276	4
α-helix	280-282	3
α-helix	283-292	10
β-strand	296-301	6	31
α-helix	306-311	6
β-strand	319-323	5	31
α-helix	331-343	13
β-strand	345-346	2	34
β-strand	348-352	5	30
β-strand	359-364	6	29
β-strand	370-371	2	29
β-strand	377-378	2	34
β-strand	386-393	8	29
β-strand	406-410	5	30
β-strand	417-423	7	30

Chain E: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-27	19
α-helix	33-35	3
α-helix	44-45	2
α-helix	46-56	11
β-strand	77-83	7	35
α-helix	84-86	3
α-helix	91-94	4
β-strand	101-105	5	36
α-helix	108-114	7
α-helix	118-120	3
β-strand	121-130	10	35
β-strand	137-143	7	36
β-strand	151-158	8	36
β-strand	165-170	6	35
α-helix	172-181	10
β-strand	187-192	6	36
β-strand	207	1	35
α-helix	216-218	3
α-helix	221-223	3
β-strand	228-233	6	35
α-helix	236-238	3
β-strand	265-268	4	37
β-strand	271	1	38
α-helix	273-277	5
β-strand	282-284	3	39
β-strand	288	1	38
β-strand	291-294	4	37
α-helix	311-314	4
α-helix	319-322	4
β-strand	327-341	15	39
β-strand	344-360	17	39

Chain F: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	10-27	18
α-helix	33-35	3
α-helix	43-45	3
α-helix	46-56	11
β-strand	77-83	7	39
α-helix	84-86	3
β-strand	101-107	7	40
α-helix	108-114	7
α-helix	118-120	3
β-strand	121-130	10	39
β-strand	138-144	7	40
β-strand	150-157	8	40
β-strand	165-170	6	39
α-helix	172-181	10
β-strand	185-192	8	40
β-strand	207	1	39
β-strand	228-233	6	39
α-helix	236-238	3
β-strand	265-267	3	41
β-strand	270-272	3	42
α-helix	273-277	5
β-strand	282-284	3	35
β-strand	287-289	3	42
β-strand	292-294	3	41
α-helix	311-317	7
β-strand	327-341	15	35
β-strand	344-360	17	35

Chain I: 10 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
β-strand	32-34	3	1
β-strand	53-55	3	1
β-strand	64	1	2
α-helix	66-70	5
β-strand	77-79	3	1
β-strand	88	1	2
α-helix	93-95	3
β-strand	102-103	2	1
α-helix	109-111	3
β-strand	129-130	2	1
α-helix	140-144	5
β-strand	154-155	2	1
β-strand	163-164	2	3
β-strand	177-179	3	1
β-strand	187-188	2	3
β-strand	201-203	3	1
β-strand	222-224	3	1
β-strand	247-249	3	1
α-helix	258-260	3
β-strand	270-271	2	4
β-strand	319-321	3	4
α-helix	334-337	4
β-strand	343-345	3	4
β-strand	353-354	2	5
β-strand	367-369	3	4
β-strand	377-378	2	5
β-strand	390-392	3	4
β-strand	414-416	3	4
β-strand	424	1	6
β-strand	437	1	6
β-strand	447-449	3	4
β-strand	457	1	7
β-strand	470-472	3	4
β-strand	480	1	7
α-helix	481-482	2
β-strand	495	1	4
α-helix	510-512	3
β-strand	518	1	4
α-helix	530-531	2
β-strand	532	1	8
β-strand	540-542	3	4
β-strand	556	1	8
β-strand	565-567	3	4
α-helix	580-586	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta activator LRRC32	I	protein	566	Homo sapiens	Q14392 (AlphaFold model)
Integrin alpha-V heavy chain	A	protein	593	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	354	Homo sapiens	P26012 (AlphaFold model)
Transforming growth factor beta-1 proprotein	E, F	protein	361	Homo sapiens	P01137 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>8VSD_1 Transforming growth factor beta activator LRRC32 (chains I)
CKMVDKKVSCQVLGLLQVPSVLPPDTETLDLSGNQLRSILASPLGFYTALRHLDLSTNEI
SFLQPGAFQALTHLEHLSLAHNRLAMATALSAGGLGPLPRVTSLDLSGNSLYSGLLERLL
GEAPSLHTLSLAENSLTRLTRHTFRDMPALEQLDLHSNVLMDIEDGAFEGLPRLTHLNLS
RNSLTCISDFSLQQLRVLDLSCNSIEAFQTASQPQAEFQLTWLDLRENKLLHFPDLAALP
RLIYLNLSNNLIRLPTGPPQDSKGIHAPSEGWSALPLSAPSGNASGRPLSQLLNLDLSYN
EIELIPDSFLEHLTSLCFLNLSRNCLRTFEARRLGSLPCLMLLDLSHNALETLELGARAL
GSLRTLLLQGNALRDLPPYTFANLASLQRLNLQGNRVSPCGGPDEPGPSGCVAFSGITSL
RSLSLVDNEIELLRAGAFLHTPLTELDLSSNPGLEVATGALGGLEASLEVLALQGNGLMV
LQVDLPCFICLKRLNLAENRLSHLPAWTQAVSLEVLDLRNNSFSLLPGSAMGGLETSLRR
LYLQGNPLSCCGNGWLAAQLHQGRVD

Sequence of entity 2 (A), FASTA

>8VSD_2 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHIL

Sequence of entity 3 (B), FASTA

>8VSD_3 Integrin beta-8 (chains B)
INTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNNIEKLNSVGNDL
SRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPHGYIHVLSLTEN
ITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLVMTDQTSHLALD
SKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFAVQGKQFHWYKD
LLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFNITAICPDGSRK
PGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIHIHRNC

Sequence of entity 4 (E, F), FASTA

>8VSD_4 Transforming growth factor beta-1 proprotein (chains E, F)
LSTCKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGEVPPGPLPEAVLALYNSTRDRVA
GESAEPEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYMFFNTSELREAVPEPVL
LSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSPEWLSFDVTGVVRQWLS
RGGEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGMNRPFLLLMATPLERAQ
HLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHEPKGYHANFCLGPCPYI
WSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRKPKVEQLSNMIVRSCKC
S

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
CA	Calcium ion	Ca	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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 Q14392 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C7H 2.7 Å, Cryo-EM Map of the latTGF-beta LHG-10 Fab complex
8VSB 2.93 Å, L-tgf-b3/GARP
8REW 2.98 Å, CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an…
8VSC 3.0 Å, L-tgf-b1/GARP
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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