6OM2: Integrin alpha-V

Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide. Determined by X-ray diffraction at 2.77 Å resolution. Released 11 Dec 2019.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 6
Atoms: 15,335
Mol. weight: 238.13 kDa
Ligands: GLY, MG, NAG, CA
Released: 11 Dec 2019

Explore 6OM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OM2 contains 62 α-helices and 159 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: 13 helices, 58 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	1	5
β-strand	127-132	6	6
β-strand	135-139	5	6
β-strand	160-162	3	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	207-209	3	7
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	8
β-strand	225-229	5	9
α-helix	237	1
β-strand	238-243	6	9
α-helix	247-249	3
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	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	372-377	6	13
β-strand	378-379	2	14
β-strand	382-383	2	14
β-strand	389-392	4	13
α-helix	393	1
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	441-451	11	15
β-strand	454-455	2	16
β-strand	462-463	2	17
β-strand	470-471	2	17
β-strand	473-485	13	15
β-strand	491-493	3	18
β-strand	494-500	7	19
α-helix	509-510	2
β-strand	512-514	3	15
β-strand	521-524	4	19
β-strand	527-529	3	18
β-strand	535-543	9	15
α-helix	544-545	2
α-helix	546-548	3
β-strand	556-564	9	19
β-strand	578-579	2	15
β-strand	586-591	6	19
β-strand	592-593	2	16

Chain B: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	76-77	2	20
β-strand	93-95	3	21
β-strand	96-97	2	20
β-strand	105-112	8	22
α-helix	115-117	3
α-helix	118-124	7
α-helix	130-139	10
β-strand	142-149	8	22
α-helix	162-165	4
α-helix	170-172	3
β-strand	176	1	23
α-helix	177-179	3
β-strand	182-189	8	22
α-helix	192-200	9
β-strand	204	1	23
β-strand	212	1	24
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-241	7	22
β-strand	246	1	24
α-helix	249-255	7
α-helix	260-261	2
β-strand	267	1	25
β-strand	271	1	22
β-strand	272	1	25
α-helix	274-276	3
α-helix	279-282	4
α-helix	283-292	10
β-strand	295-301	7	22
α-helix	306-310	5
α-helix	313-315	3
β-strand	320-323	4	22
α-helix	324-325	2
α-helix	331-344	14
β-strand	348-349	2	26
β-strand	359-363	5	21
β-strand	388-392	5	21
β-strand	409-410	2	26

Chain C: 13 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	9-12	4	28
β-strand	23-26	4	29
β-strand	35-40	6	29
β-strand	55-60	6	29
β-strand	67-69	3	29
β-strand	79-81	3	30
β-strand	84-85	2	30
β-strand	87-88	2	31
β-strand	97-101	5	32
β-strand	104-109	6	32
β-strand	113-114	2	31
β-strand	123	1	31
β-strand	127-132	6	32
β-strand	135-139	5	32
β-strand	160-163	4	33
β-strand	168	1	34
β-strand	169-172	4	33
α-helix	176-179	4
β-strand	181	1	35
β-strand	183-185	3	33
β-strand	187	1	34
α-helix	188-193	6
β-strand	208-209	2	33
α-helix	215-217	3
β-strand	222	1	35
β-strand	225-229	5	36
α-helix	237	1
β-strand	238-243	6	36
β-strand	252-256	5	36
β-strand	263-268	6	36
β-strand	280-283	4	37
β-strand	292-297	6	37
β-strand	301	1	38
β-strand	311	1	38
β-strand	314-320	7	37
α-helix	321	1
β-strand	326-332	7	37
β-strand	344-348	5	39
β-strand	357-362	6	39
α-helix	367-369	3
β-strand	372-376	5	39
β-strand	378-379	2	40
β-strand	382-383	2	40
β-strand	389-392	4	39
β-strand	408-413	6	28
β-strand	422-427	6	28
α-helix	428-430	3
β-strand	432-436	5	28
α-helix	437	1
β-strand	438	1	27
α-helix	439-440	2
β-strand	441-451	11	41
β-strand	454-455	2	42
β-strand	463	1	43
β-strand	470	1	43
β-strand	473-484	12	41
β-strand	491-500	10	44
α-helix	509-510	2
β-strand	512-514	3	41
β-strand	521-529	9	44
β-strand	535-543	9	41
α-helix	546-548	3
β-strand	556-564	9	44
α-helix	566-569	4
β-strand	578-579	2	41
β-strand	587-591	5	44
β-strand	592-593	2	42
α-helix	594-595	2

Chain D: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	76-77	2	45
β-strand	92-93	2	46
β-strand	96-97	2	45
β-strand	105-112	8	47
α-helix	115-117	3
α-helix	118-124	7
α-helix	127-135	9
β-strand	142-149	8	47
α-helix	162-165	4
α-helix	170-172	3
β-strand	176	1	48
α-helix	177-179	3
β-strand	183-189	7	47
α-helix	192-200	9
β-strand	204	1	48
β-strand	212	1	49
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	47
β-strand	246	1	49
α-helix	249-255	7
α-helix	260-261	2
β-strand	267	1	50
β-strand	271	1	47
β-strand	272	1	50
α-helix	274-276	3
α-helix	279-282	4
α-helix	283-292	10
β-strand	295-301	7	47
α-helix	306-310	5
α-helix	313-315	3
β-strand	319-323	5	47
α-helix	331-344	14
β-strand	348-349	2	51
β-strand	360-361	2	46
β-strand	362-364	3	52
β-strand	370-372	3	52
α-helix	373-375	3
β-strand	387	1	52
β-strand	390-391	2	46
β-strand	406-408	3	53
β-strand	409-410	2	51
β-strand	417-419	3	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A, C	protein	598	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B, D	protein	421	Homo sapiens	P26012 (AlphaFold model)
proTGF-beta1 RGD peptide	E, F	protein	11	Homo sapiens	P01137 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OM2_1 Integrin alpha-V (chains A, C)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGY
PDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCL
KADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELI
AYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLTGG

Sequence of entity 2 (B, D), FASTA

>6OM2_2 Integrin beta-8 (chains B, D)
EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYP
SVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNN
IEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPH
GYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLV
MTDQTSHLALDSKLAGIVCPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFA
VQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFN
ITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIH
I

Sequence of entity 3 (E, F), FASTA

>6OM2_3 proTGF-beta1 RGD peptide (chains E, F)
GRRGDLATIHG

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	1
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CA	Calcium ion	Ca	10

Water and common crystallization additives (PEG) are not listed.

Primary citation

General structural features that regulate integrin affinity revealed by atypical alpha V beta 8. Wang, J., Su, Y., Iacob, R.E. et al. Nat Commun (2019) 10:5481-5481. DOI 10.1038/s41467-019-13248-5 · 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
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
8XEL 2.8 Å, Cryo-EM structure of integrin ITGAV/ITGB3 complex, conformation 3

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