8TCG: Integrin alpha-v beta-6

Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf. Determined by electron microscopy at 3.4 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 5,945
Mol. weight: 84.78 kDa
Ligands: MN, NAG, CA
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8TCG contains 26 α-helices and 58 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: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	23-26	4	2
α-helix	32-34	3
β-strand	35-40	6	2
β-strand	55-60	6	2
β-strand	67-69	3	2
α-helix	77-78	2
β-strand	79-81	3	3
β-strand	84-85	2	3
β-strand	87-88	2	4
β-strand	97-101	5	5
β-strand	104-109	6	5
β-strand	113-114	2	4
β-strand	123	1	4
β-strand	127-132	6	5
β-strand	135-139	5	5
β-strand	160-163	4	6
β-strand	168-173	6	6
α-helix	176-179	4
β-strand	181	1	7
β-strand	182-187	6	6
α-helix	188-193	6
β-strand	208-209	2	6
α-helix	215-217	3
β-strand	222	1	7
β-strand	226-229	4	8
β-strand	238-243	6	8
α-helix	246-249	4
β-strand	252-256	5	8
β-strand	263-268	6	8
β-strand	280-283	4	9
β-strand	292-297	6	9
β-strand	301-303	3	10
β-strand	309-311	3	10
β-strand	314-320	7	9
β-strand	326-332	7	9
β-strand	343-348	6	11
β-strand	357-362	6	11
α-helix	367-369	3
β-strand	372-376	5	11
β-strand	378-379	2	12
β-strand	382-383	2	12
β-strand	389-392	4	11
α-helix	393	1
β-strand	409-413	5	1
β-strand	422-427	6	1
α-helix	428-430	3
β-strand	432-438	7	1
α-helix	439	1

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	116-123	8	13
α-helix	126-128	3
α-helix	132-146	15
β-strand	153-160	8	13
α-helix	173-177	5
β-strand	188	1	14
α-helix	189-190	2
β-strand	193-200	8	13
α-helix	203-211	9
β-strand	216	1	14
β-strand	223	1	15
α-helix	225-234	10
α-helix	236-239	4
β-strand	246-252	7	13
β-strand	257	1	15
α-helix	262-266	5
β-strand	270	1	16
β-strand	278	1	17
β-strand	283	1	13
β-strand	284	1	17
β-strand	290	1	16
α-helix	291-294	4
α-helix	295-304	10
β-strand	307-313	7	13
α-helix	315-325	11
β-strand	332-335	4	13
α-helix	341-349	9

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	18
α-helix	14-28	15
β-strand	33-37	5	18
α-helix	38-40	3
β-strand	42-46	5	18
α-helix	52-54	3
α-helix	56-63	8
β-strand	68-72	5	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A	protein	440	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	242	Homo sapiens	P18564 (AlphaFold model)
Minibinder B6_BP_dslf	C	protein	72	synthetic construct

Sequence of entity 1 (A), FASTA

>8TCG_1 Integrin alpha-V heavy chain (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGY
PDLIVGAFGVDRAILYRARP

Sequence of entity 2 (B), FASTA

>8TCG_2 Integrin beta-6 (chains B)
DYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTT
PEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQA
AVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEY
PTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYE
EL

Sequence of entity 3 (C), FASTA

>8TCG_3 Minibinder B6_BP_dslf (chains C)
CVVRFVFRGDLAELMLRAVKDHLKKEGPHWNITSTNNGKELVVRGIHESDAKRIAKWVEK
RFPRVHTETQCD

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	4

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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