8TCF: Integrin alpha-v beta-8

Integrin alpha-v beta-8 in complex with minibinder B8_BP_dsulf. Determined by electron microscopy at 2.9 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 7,050
Mol. weight: 100.62 kDa
Ligands: MG, NAG, CA
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8TCF contains 31 α-helices and 66 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, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	23-26	4	3
β-strand	35-40	6	3
β-strand	55-59	5	3
β-strand	67-69	3	3
α-helix	77-78	2
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	1	5
β-strand	127-132	6	6
β-strand	135-139	5	6
β-strand	160-164	5	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	280-283	4	10
β-strand	292-297	6	10
β-strand	301-303	3	11
β-strand	309-311	3	11
β-strand	314-320	7	10
β-strand	326-332	7	10
β-strand	343-348	6	12
β-strand	357-362	6	12
α-helix	367-369	3
β-strand	372-376	5	12
β-strand	389-392	4	12
β-strand	409-413	5	2
β-strand	422-427	6	2
α-helix	428-430	3
β-strand	432-436	5	2
α-helix	437	1
β-strand	438	1	1
α-helix	439-440	2

Chain B: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	13
α-helix	70-71	2
β-strand	76-77	2	14
β-strand	80-85	6	13
β-strand	90-97	8	14
α-helix	99-100	2
β-strand	103-112	10	15
α-helix	115-117	3
α-helix	121-126	6
α-helix	129-134	6
α-helix	135-137	3
β-strand	139-149	11	15
α-helix	170-172	3
α-helix	176-179	4
β-strand	182-189	8	15
α-helix	192-200	9
α-helix	202-204	3
β-strand	212	1	16
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	15
α-helix	245	1
β-strand	246	1	16
α-helix	247-248	2
α-helix	251-255	5
β-strand	267	1	17
β-strand	271	1	15
β-strand	272	1	17
α-helix	280-282	3
α-helix	283-292	10
β-strand	295-301	7	15
α-helix	306-310	5
α-helix	313-315	3
β-strand	319-323	5	15
α-helix	331-342	12
β-strand	346	1	18
β-strand	348-352	5	13
β-strand	357-364	8	14
β-strand	370-372	3	14
β-strand	377	1	18
β-strand	386-394	9	14
β-strand	405-410	6	13
β-strand	417-423	7	13

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	19
α-helix	14-28	15
β-strand	33-37	5	19
β-strand	42-49	8	19
α-helix	52-62	11
β-strand	69-74	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A	protein	444	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	359	Homo sapiens	P26012 (AlphaFold model)
Minibinder B8_BP_dslf	C	protein	75	synthetic construct

Sequence of entity 1 (A), FASTA

>8TCF_1 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGY
PDLIVGAFGVDRAILYRARPVITV

Sequence of entity 2 (B), FASTA

>8TCF_2 Integrin beta-8 (chains B)
VHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNNI
EKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPHG
YIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLVM
TDQTSHLALDSKLAGIVCPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFAV
QGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFNI
TAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDNYAIIKPIGFNETAKIHIHRNC

Sequence of entity 3 (C), FASTA

>8TCF_3 Minibinder B8_BP_dslf (chains C)
TKCVVRFNFRGDMAVYALKAVKDHLKKEGPHWNITTHNDDEVYLVVRGIHESDAKRIAKW
VESTIPGISVETQCD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
CA	Calcium ion	Ca	5

Primary citation

De novo design of highly selective miniprotein inhibitors of integrins alpha v beta 6 and alpha v beta 8. Roy, A., Shi, L., Chang, A. et al. Nat Commun (2023) 14:5660-5660. DOI 10.1038/s41467-023-41272-z · 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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