9IND: Integrin alpha-v beta-8

Integrin alpha-v beta-8 in complex with the Fab of 130H2. Determined by electron microscopy at 2.88 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 7,644
Mol. weight: 113.72 kDa
Ligands: NAG
Released: 22 Jan 2025

Explore 9IND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IND contains 26 α-helices and 94 β-strands across 4 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: 6 helices, 43 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	55-60	6	3
β-strand	67-69	3	3
β-strand	79-81	3	4
β-strand	84-85	2	4
β-strand	87-88	2	5
β-strand	97-101	5	6
β-strand	104-109	6	6
β-strand	113-114	2	5
β-strand	123-124	2	5
β-strand	127-132	6	6
β-strand	135-139	5	6
β-strand	160-163	4	7
β-strand	168-173	6	7
α-helix	176-179	4
β-strand	181	1	8
β-strand	182-187	6	7
α-helix	188-193	6
β-strand	208-209	2	7
α-helix	215-217	3
β-strand	222	1	8
β-strand	225-229	5	9
β-strand	238-243	6	9
α-helix	246-249	4
β-strand	252-256	5	9
β-strand	263-268	6	9
β-strand	279-283	5	10
β-strand	292-297	6	10
β-strand	301-303	3	11
β-strand	309-311	3	11
β-strand	313	1	12
β-strand	314-320	7	10
β-strand	326-332	7	10
β-strand	340	1	12
β-strand	343-348	6	13
β-strand	357-362	6	13
α-helix	367-369	3
β-strand	372-376	5	13
β-strand	378-379	2	14
β-strand	382-383	2	14
β-strand	389-392	4	13
β-strand	407-412	6	2
β-strand	421-426	6	2
β-strand	431-435	5	2
β-strand	437	1	1
α-helix	438-439	2

Chain B: 16 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	76-77	2	21
β-strand	80-82	3	22
β-strand	91-97	7	21
α-helix	99-100	2
β-strand	103-112	10	23
α-helix	115-117	3
α-helix	118-122	5
α-helix	127-131	5
α-helix	132-134	3
α-helix	135-137	3
β-strand	139-149	11	23
α-helix	162-171	10
β-strand	176	1	24
β-strand	182-189	8	23
α-helix	192-201	10
β-strand	204	1	24
β-strand	212	1	25
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	23
β-strand	246	1	25
α-helix	251-255	5
β-strand	259	1	26
α-helix	260-261	2
β-strand	267	1	27
β-strand	271	1	23
β-strand	272	1	27
β-strand	278	1	26
α-helix	280-282	3
α-helix	283-292	10
β-strand	295-301	7	23
α-helix	306-312	7
β-strand	319-323	5	23
α-helix	331-344	14
β-strand	346	1	28
β-strand	348-351	4	22
β-strand	357-364	8	21
β-strand	370-372	3	21
β-strand	377	1	28
β-strand	386-394	9	21
β-strand	405-410	6	22
β-strand	418-420	3	22

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	15
β-strand	10-11	2	16
β-strand	17-23	7	15
β-strand	33-39	7	16
β-strand	45-52	8	16
β-strand	58-60	3	16
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-100	9	16
β-strand	103-108	6	16
β-strand	113-116	4	16

Chain L: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	17
β-strand	10	1	18
β-strand	19-23	5	17
β-strand	29	1	19
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	17
β-strand	68	1	19
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102	1	20
β-strand	103	1	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A	protein	440	Homo sapiens	P06756 (AlphaFold model)
The heavy chain of 130H2-Fab	H	protein	119	Mus musculus
The light chain of 130H2-Fab	L	protein	104	Mus musculus
Integrin beta-8	B	protein	352	Homo sapiens	P26012 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9IND_1 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGWP
DLIVGAFGVDRAILYRARPV

Sequence of entity 2 (H), FASTA

>9IND_2 The heavy chain of 130H2-Fab (chains H)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTNYGINWVRQAPGQGLEWMGYFYIGNGYTEY
NEKFKGRVTMTSDTSTSTVYMELSSLRSEDTAVYYCALNYFGSRKFDYWGQGTTVTVSS

Sequence of entity 3 (L), FASTA

>9IND_3 The light chain of 130H2-Fab (chains L)
EIVLTQSPATLSLSPGERATLSCRASQNIITNLHWYQQKPGQAPRLLIKYASQSISGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYFCQQSDDWPLTFGQGTKL

Sequence of entity 4 (B), FASTA

>9IND_4 Integrin beta-8 (chains B)
NEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNNIEKLNSVGN
DLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPHGYIHVLSLT
ENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLVMTDQTSHLA
LDSKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFAVQGKQFHWY
KDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFNITAICPDGS
RKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIHI

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Specifically blocking alpha v beta 8-mediated TGF-beta signaling to reverse immunosuppression by modulating macrophage polarization. Guo, C., Sun, H., Du, Y. et al. J Exp Clin Cancer Res (2025) 44:1-1. DOI 10.1186/s13046-024-03250-1 · PubMed

Other PDB entries of the same protein (UniProt P06756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CZD 2.23 Å, Crystal structure of integrin avb6 headpiece in complex with compound 30
5FFG 2.25 Å, Crystal structure of integrin alpha V beta 6 head
8W30 2.45 Å, Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179
9CZA 2.49 Å, Crystal structure of integrin avb6 headpiece in complex with compound 18
4UM9 2.5 Å, Crystal structure of alpha V beta 6 with peptide
9CZF 2.53 Å, Crystal structure of integrin avb6 headpiece in complex with compound MORF-627
9CZ7 2.57 Å, Crystal structure of integrin avb6 headpiece in complex with compound 12
6OM1 2.66 Å, Crystal structure of an atypical integrin
8VS6 2.73 Å, L-TGF-b3/avb8
6OM2 2.77 Å, Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide
9IUJ 2.78 Å, Integrin alpha-v beta-3 in complex with rhodostomin
9LT3 2.79 Å, Integrin alpha-v beta-3 in complex with Trimucrin

Browse structure collections

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