7Y1T: Integrin alpha-V

Complex of integrin alphaV/beta8 and L-TGF-beta1 at a ratio of 1:2. Determined by electron microscopy at 3.24 Å resolution. Released 31 Aug 2022.

Method: Electron microscopy
Resolution: 3.24 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,112
Mol. weight: 169.75 kDa
Ligands: NAG, CA, MN
Released: 31 Aug 2022

Explore 7Y1T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y1T contains 30 α-helices and 75 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: 11 helices, 46 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	70-71	2
β-strand	79-81	3	4
β-strand	84-85	2	4
β-strand	87-88	2	5
β-strand	97-100	4	6
β-strand	105-109	5	6
β-strand	113-114	2	5
α-helix	115-116	2
β-strand	124	1	5
β-strand	127-131	5	6
β-strand	136-139	4	6
α-helix	148-151	4
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	1	7
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	8
β-strand	226-229	4	9
β-strand	238-243	6	9
α-helix	246-249	4
β-strand	252-256	5	9
β-strand	266-268	3	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	314-320	7	10
β-strand	326-332	7	10
β-strand	343-348	6	12
β-strand	357-362	6	12
β-strand	372-376	5	12
β-strand	389-392	4	12
β-strand	408-413	6	2
β-strand	422-427	6	2
β-strand	432-436	5	2
α-helix	437	1
β-strand	438	1	1
α-helix	439-440	2
β-strand	441-450	10	13
β-strand	476-484	9	13
β-strand	491-496	6	14
β-strand	524-529	6	14
β-strand	537-539	3	13
β-strand	563-564	2	14
α-helix	575-577	3
β-strand	578-579	2	13

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	76	1	15
β-strand	82-84	3	16
β-strand	91-97	7	15
β-strand	105-112	8	17
α-helix	115-117	3
α-helix	120-123	4
α-helix	124-126	3
α-helix	127-135	9
β-strand	142-149	8	17
α-helix	170-172	3
α-helix	177-179	3
β-strand	183-189	7	17
α-helix	193-201	9
α-helix	215-223	9
α-helix	225-228	4
β-strand	235-242	8	17
α-helix	245-247	3
α-helix	249-253	5
β-strand	267	1	18
β-strand	271	1	17
β-strand	272	1	18
α-helix	280-282	3
α-helix	283-292	10
β-strand	296-301	6	17
α-helix	306-311	6
β-strand	319-323	5	17
α-helix	331-344	14
β-strand	346	1	19
β-strand	348-351	4	16
β-strand	357-358	2	20
β-strand	361-364	4	15
β-strand	377	1	19
α-helix	385	1
β-strand	386-392	7	15
β-strand	393-394	2	20
β-strand	405-410	6	16
β-strand	417-422	6	16

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	78-83	6	21
α-helix	87-91	5
β-strand	102-106	5	22
α-helix	108-114	7
β-strand	121-129	9	21
β-strand	139-145	7	22
β-strand	149-156	8	22
β-strand	166-170	5	21
α-helix	172-179	8
β-strand	186-192	7	22
β-strand	228-233	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A	protein	635	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	477	Homo sapiens	P26012 (AlphaFold model)
Transforming growth factor beta-1 proprotein	D	protein	377	Homo sapiens	P01137 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7Y1T_1 Integrin alpha-V (chains A)
MAFPPRRRLRLGPRGLPLLLSGLLLPLCRAFNLDVDSPAEYSGPEGSYFGFAVDFFVPSA
SSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKS
HQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDAD
GQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLAT
RTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGE
QMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTK
LNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQI
LEGQWAARSGCPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEV
YPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKQKGAIR
RALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAA
DTTGLQPILNQFTPANISRQAHILLDTGGLEVLFQ

Sequence of entity 2 (B), FASTA

>7Y1T_2 Integrin beta-8 (chains B)
MDMRVPAQLLGLLLLWFSGVLEDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSE
RCDIVSNLISKGCSVDSIEYPSVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHP
LKKYPVDLYYLVDVSASMHNNIEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYIS
IHPERIHNQCSDYNLDCMPPHGYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAML
QAAVCESHIGWRKEAKRLLLVMTDQTSHLALDSKLAGIVCPNDGNCHLKNNVYVKSTTME
HPSLGQLSEKLIDNNINVIFAVQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAY
QKLISEVKVQVENQVQGIYFNITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDV
TGGKNYAIIKPIGFNETAKIHIHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENK

Sequence of entity 3 (D), FASTA

>7Y1T_3 Transforming growth factor beta-1 proprotein (chains D)
MPLLLLLPLLWAGALALSTCKTIDMELVKRKRIEAIRGQILSKLRLASPPSQGEVPPGPL
PEAVLALYNSTRDRVAGESAEPEPEPEADYYAKEVTRVLMVETHNEIYDKFKQSTHSIYM
FFNTSELREAVPEPVLLSRAELRLLRLKLKVEQHVELYQKYSNNSWRYLSNRLLAPSDSP
EWLSFDVTGVVRQWLSRGGEIEGFRLSAHCSCDSRDNTLQVDINGFTTGRRGDLATIHGM
NRPFLLLMATPLERAQHLQSSRHRRALDTNYCFSSTEKNCCVRQLYIDFRKDLGWKWIHE
PKGYHANFCLGPCPYIWSLDTQYSKVLALYNQHNPGASAAPCCVPQALEPLPIVYYVGRK
PKVEQLSNMIVRSCKCS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
CA	Calcium ion	Ca	5
MN	Manganese (II) ion	Mn	1

Primary citation

Specificity of TGF-beta 1 signal designated by LRRC33 and integrin alpha V beta 8. Duan, Z., Lin, X., Wang, L. et al. Nat Commun (2022) 13:4988-4988. DOI 10.1038/s41467-022-32655-9 · 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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