8VS6: L-TGF-b3/avb8

L-TGF-b3/avb8. Determined by electron microscopy at 2.73 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.73 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,438
Mol. weight: 226.16 kDa
Ligands: NAG, CA, MG
Released: 11 Sept 2024

Explore 8VS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VS6 contains 30 α-helices and 69 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: 9 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	22-26	5	3
β-strand	35-40	6	3
β-strand	54	1	4
β-strand	55-60	6	3
β-strand	67-69	3	3
β-strand	79-81	3	5
β-strand	84-85	2	5
β-strand	87-88	2	6
β-strand	94	1	4
β-strand	97-100	4	7
β-strand	104-109	6	7
β-strand	113-114	2	6
β-strand	123	1	6
β-strand	127-132	6	7
β-strand	135-139	5	7
β-strand	160-163	4	8
β-strand	168-173	6	8
α-helix	176-179	4
β-strand	181	1	9
β-strand	182-187	6	8
α-helix	188-193	6
β-strand	208-209	2	8
α-helix	215-217	3
β-strand	222	1	9
β-strand	225-229	5	10
α-helix	237	1
β-strand	238-243	6	10
α-helix	246-249	4
β-strand	251	1	11
β-strand	252-256	5	10
β-strand	263-268	6	10
β-strand	276	1	11
β-strand	279-283	5	12
β-strand	292-297	6	12
β-strand	301-303	3	13
β-strand	309-311	3	13
β-strand	313	1	14
β-strand	314-321	8	12
β-strand	325-332	8	12
β-strand	340	1	14
β-strand	343-348	6	15
β-strand	357-362	6	15
α-helix	367-369	3
β-strand	372-376	5	15
β-strand	378	1	16
β-strand	383	1	16
β-strand	389-392	4	15
α-helix	396-397	2
β-strand	407-412	6	2
β-strand	421-426	6	2
β-strand	431-435	5	2
α-helix	436	1
β-strand	437	1	1
α-helix	438-439	2

Chain B: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	76-77	2	17
β-strand	80-85	6	18
β-strand	90-97	8	17
β-strand	103-112	10	19
α-helix	115-117	3
α-helix	118-121	4
α-helix	122-126	5
α-helix	129-135	7
β-strand	139-149	11	19
α-helix	162-166	5
α-helix	176-179	4
β-strand	182-189	8	19
α-helix	192-201	10
β-strand	212	1	20
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	19
α-helix	245	1
β-strand	246	1	20
α-helix	247-248	2
α-helix	249-255	7
α-helix	260-261	2
β-strand	267	1	21
β-strand	271	1	19
β-strand	272	1	21
α-helix	273-276	4
α-helix	279-282	4
α-helix	283-292	10
β-strand	296-301	6	19
α-helix	306-310	5
α-helix	313-315	3
β-strand	319-323	5	19
α-helix	324-325	2
α-helix	331-343	13
β-strand	345-346	2	22
β-strand	348-350	3	18
β-strand	357-364	8	17
β-strand	370-371	2	17
β-strand	377-378	2	22
β-strand	386-394	9	17
β-strand	405-410	6	18
β-strand	417-423	7	18

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	245-248	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming growth factor beta-3 proprotein	E	protein	389	Homo sapiens	P10600 (AlphaFold model)
Integrin alpha-V	A	protein	962	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	642	Homo sapiens	P26012 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>8VS6_1 Transforming growth factor beta-3 proprotein (chains E)
LSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEM
HGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNR
TNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFD
VTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGD
LGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKRALDTNYCFRNLEENCCVRPLYID
FRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDL
EPLTILYYVGRTPKVEQLSNMVVKSCKCS

Sequence of entity 2 (A), FASTA

>8VS6_2 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPAPM
PV

Sequence of entity 3 (B), FASTA

>8VS6_3 Integrin beta-8 (chains B)
EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYP
SVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNN
IEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPH
GYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLV
MTDQTSHLALDSKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFA
VQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFN
ITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIH
IHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENKCHFDEDQFSSESCKSHKDQPVCSG
RGVCVCGKCSCHKIKLGKVYGKYCEKDDFSCPYHHGNLCAGHGECEAGRCQCFSGWEGDR
CQCPSAAAQHCVNSKGQVCSGRGTCVCGRCECTDPRSIGRFCEHCPTCYTACKENWNCMQ
CLHPHNLSQAILDQCKTSCALMEQQHYVDQTSECFSSPSYLR

Ligands and cofactors

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

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 P10600 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TGJ 2.0 Å, Human transforming growth factor-beta 3, crystallized from dioxane
1KTZ 2.15 Å, Crystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex…
4UM9 2.5 Å, Crystal structure of alpha V beta 6 with peptide
8V52 2.5 Å, Crystal structure of 2A10 Fab bound to Human TGF-beta3
8VSB 2.93 Å, L-tgf-b3/GARP
2PJY 3.0 Å, Structural basis for cooperative assembly of the TGF-beta signaling complex
9B9F 3.0 Å, Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular…
3EO1 3.1 Å, Structure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
1TGK 3.3 Å, Human transforming growth factor beta 3, crystallized from peg 4000
9FK5 4.1 Å, Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular…

Browse structure collections

About this viewer

MolViewer shows 8VS6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.