6OM1: Atypical integrin

Crystal structure of an atypical integrin. Determined by X-ray diffraction at 2.66 Å resolution. Released 11 Dec 2019.

Method: X-ray diffraction
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 8
Atoms: 30,588
Mol. weight: 488.65 kDa
Ligands: MG, CA, NAG
Released: 11 Dec 2019

Explore 6OM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OM1 contains 107 α-helices and 309 β-strands across 8 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, 55 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	127-131	5	6
β-strand	136-139	4	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	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	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	344-348	5	12
β-strand	357-362	6	12
α-helix	367-369	3
β-strand	372-377	6	12
β-strand	378-379	2	13
β-strand	382-383	2	13
β-strand	389-392	4	12
β-strand	408-413	6	2
β-strand	422-427	6	2
α-helix	428-430	3
β-strand	432-436	5	2
β-strand	438	1	1
α-helix	439-440	2
β-strand	441-451	11	14
β-strand	454-455	2	15
β-strand	462-463	2	16
β-strand	470-471	2	16
β-strand	473-484	12	14
β-strand	491-500	10	17
β-strand	513-514	2	14
β-strand	521-529	9	17
β-strand	530	1	14
β-strand	535-542	8	14
β-strand	556-564	9	17
α-helix	566-569	4
β-strand	578-579	2	14
β-strand	586-591	6	17
β-strand	592-593	2	15

Chain B: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	68	1	18
β-strand	77	1	19
β-strand	80-81	2	18
β-strand	93-97	5	19
β-strand	105-112	8	20
α-helix	115-117	3
α-helix	118-123	6
α-helix	128-138	11
β-strand	142-149	8	20
α-helix	177-179	3
β-strand	182-189	8	20
α-helix	193-200	8
β-strand	212	1	21
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-241	7	20
α-helix	245	1
β-strand	246	1	21
α-helix	247	1
α-helix	250-255	6
β-strand	267	1	22
β-strand	271	1	20
β-strand	272	1	22
α-helix	279-282	4
α-helix	283-293	11
β-strand	295-301	7	20
α-helix	306-311	6
α-helix	313-315	3
β-strand	319-323	5	20
α-helix	331-342	12
β-strand	345	1	23
β-strand	348-351	4	18
β-strand	358-364	7	19
β-strand	378	1	23
β-strand	386-393	8	19
β-strand	406-410	5	18
β-strand	417-419	3	18

Chain C: 14 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
α-helix	8	1
β-strand	9-12	4	25
β-strand	22-26	5	26
β-strand	35-40	6	26
β-strand	55-60	6	26
β-strand	67-70	4	26
β-strand	79-81	3	27
β-strand	84-85	2	27
β-strand	87-88	2	28
β-strand	97-101	5	29
β-strand	104-109	6	29
β-strand	113-114	2	28
β-strand	123	1	28
β-strand	127-131	5	29
β-strand	136-139	4	29
β-strand	160-163	4	30
β-strand	168-173	6	30
α-helix	176-179	4
β-strand	181	1	31
β-strand	182-187	6	30
α-helix	188-193	6
α-helix	202-204	3
β-strand	208-209	2	30
α-helix	215-217	3
β-strand	222	1	31
β-strand	225-229	5	32
α-helix	237	1
β-strand	238-243	6	32
α-helix	246-249	4
β-strand	252-256	5	32
β-strand	263-268	6	32
β-strand	279-283	5	33
β-strand	292-297	6	33
β-strand	301-303	3	34
β-strand	309-311	3	34
β-strand	314-320	7	33
β-strand	326-332	7	33
β-strand	343-348	6	35
β-strand	357-362	6	35
α-helix	367-369	3
β-strand	372-377	6	35
β-strand	378-379	2	36
β-strand	382-383	2	36
β-strand	389-392	4	35
β-strand	408-413	6	25
β-strand	422-427	6	25
α-helix	428-430	3
β-strand	432-436	5	25
α-helix	437	1
β-strand	438	1	24
α-helix	439-440	2
β-strand	441-442	2	37
β-strand	443-451	9	38
β-strand	454-455	2	39
β-strand	462-463	2	40
β-strand	470-471	2	40
β-strand	473-483	11	38
β-strand	491-500	10	41
β-strand	512-514	3	38
β-strand	521-529	9	41
β-strand	530	1	38
α-helix	533-534	2
β-strand	535-543	9	38
α-helix	546-548	3
β-strand	556-564	9	41
α-helix	566-569	4
β-strand	578-579	2	37
β-strand	586-591	6	41
β-strand	592-593	2	39

Chain D: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	42
β-strand	80	1	43
β-strand	93-97	5	42
β-strand	105-112	8	44
α-helix	115-117	3
α-helix	118-124	7
α-helix	131-138	8
β-strand	142-149	8	44
α-helix	177-179	3
β-strand	182-189	8	44
α-helix	192-200	9
β-strand	212	1	45
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-241	7	44
β-strand	246	1	45
α-helix	249-253	5
β-strand	259	1	46
β-strand	267	1	47
β-strand	271	1	44
β-strand	272	1	47
α-helix	273-276	4
β-strand	278	1	46
α-helix	279-282	4
α-helix	283-292	10
β-strand	295-301	7	44
α-helix	306-311	6
α-helix	313-315	3
β-strand	319-323	5	44
α-helix	331-343	13
β-strand	348-351	4	43
β-strand	359-364	6	42
β-strand	386-392	7	42
β-strand	407-410	4	43
β-strand	417-418	2	43

Chain E: 12 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	48
β-strand	22-26	5	49
β-strand	35-40	6	49
β-strand	55-59	5	49
β-strand	67-70	4	49
β-strand	79-81	3	50
β-strand	84-85	2	50
β-strand	87-88	2	51
β-strand	97-101	5	52
β-strand	104-109	6	52
β-strand	113-114	2	51
β-strand	123	1	51
β-strand	127-131	5	52
β-strand	136-139	4	52
β-strand	160-163	4	53
β-strand	168-173	6	53
α-helix	176-179	4
β-strand	181	1	54
β-strand	182-187	6	53
α-helix	188-193	6
β-strand	208-209	2	53
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	54
β-strand	225-229	5	55
α-helix	237	1
β-strand	238-243	6	55
α-helix	246-249	4
β-strand	252-256	5	55
β-strand	263-268	6	55
β-strand	279-283	5	56
β-strand	292-296	5	56
β-strand	301-303	3	57
β-strand	309-311	3	57
β-strand	313	1	58
β-strand	314-320	7	56
β-strand	326-332	7	56
β-strand	340	1	58
β-strand	343-348	6	59
β-strand	357-362	6	59
α-helix	367-369	3
β-strand	372-377	6	59
β-strand	378-379	2	60
β-strand	382-383	2	60
β-strand	389-392	4	59
β-strand	408-413	6	48
β-strand	422-427	6	48
α-helix	428-430	3
β-strand	432-438	7	48
α-helix	439-440	2
β-strand	441-451	11	61
β-strand	454	1	62
β-strand	462	1	63
β-strand	471	1	63
β-strand	473-484	12	61
β-strand	491-500	10	64
β-strand	512-514	3	61
β-strand	521-529	9	64
α-helix	533-534	2
β-strand	535-543	9	61
α-helix	546-548	3
β-strand	556-564	9	64
α-helix	566-569	4
β-strand	578-579	2	61
β-strand	586-591	6	64
β-strand	592	1	62

Chain F: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	65
β-strand	80-82	3	66
β-strand	91-97	7	65
β-strand	105-112	8	67
α-helix	115-117	3
α-helix	118-123	6
α-helix	124-126	3
α-helix	127-138	12
β-strand	142-149	8	67
β-strand	183-189	7	67
α-helix	193-201	9
β-strand	212	1	68
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	67
β-strand	246	1	68
α-helix	250-253	4
β-strand	259	1	69
β-strand	267	1	70
β-strand	271	1	67
β-strand	272	1	70
β-strand	278	1	69
α-helix	279-282	4
α-helix	283-292	10
β-strand	295-301	7	67
α-helix	306-312	7
α-helix	313-315	3
β-strand	319-323	5	67
α-helix	324-325	2
α-helix	331-342	12
β-strand	348-351	4	66
β-strand	359-364	6	65
β-strand	386-392	7	65
β-strand	405-410	6	66
β-strand	417-420	4	66

Chain G: 13 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	71
β-strand	22-26	5	72
β-strand	35-40	6	72
β-strand	54	1	73
β-strand	55-60	6	72
β-strand	67-70	4	72
β-strand	79-81	3	74
β-strand	84-85	2	74
β-strand	87-88	2	75
β-strand	94	1	73
β-strand	97-101	5	76
β-strand	104-109	6	76
β-strand	113-114	2	75
β-strand	123	1	75
β-strand	127-131	5	76
β-strand	136-139	4	76
α-helix	152-154	3
β-strand	160-163	4	77
β-strand	168-173	6	77
α-helix	176-179	4
β-strand	181	1	78
β-strand	182-187	6	77
α-helix	188-193	6
β-strand	207-209	3	77
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	78
β-strand	225-229	5	79
α-helix	237	1
β-strand	238-243	6	79
α-helix	246-249	4
β-strand	252-256	5	79
β-strand	263-268	6	79
β-strand	279-283	5	80
β-strand	292-297	6	80
β-strand	301-303	3	81
β-strand	309-311	3	81
β-strand	313	1	82
β-strand	314-320	7	80
β-strand	326-332	7	80
β-strand	340	1	82
β-strand	344-348	5	83
β-strand	357-362	6	83
α-helix	367-369	3
β-strand	372-376	5	83
β-strand	378-379	2	84
β-strand	382-383	2	84
β-strand	389-392	4	83
β-strand	405-413	9	71
β-strand	422-427	6	71
α-helix	428-430	3
β-strand	432-438	7	71
α-helix	439-440	2
β-strand	441-451	11	85
β-strand	454-455	2	86
β-strand	462-463	2	87
β-strand	470-471	2	87
β-strand	473-484	12	85
β-strand	491-500	10	88
β-strand	512-514	3	85
β-strand	521-529	9	88
β-strand	535-543	9	85
α-helix	544-545	2
α-helix	546-548	3
β-strand	556-564	9	88
α-helix	566-569	4
β-strand	578-579	2	85
β-strand	586-591	6	88
β-strand	592-593	2	86

Chain H: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	89
β-strand	80-83	4	90
β-strand	90-97	8	89
β-strand	105-112	8	91
α-helix	115-117	3
α-helix	118-122	5
α-helix	128-138	11
β-strand	142-149	8	91
β-strand	177	1	92
β-strand	182-189	8	91
α-helix	193-200	8
β-strand	205	1	92
β-strand	212	1	93
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	91
β-strand	246	1	93
α-helix	250-255	6
β-strand	267	1	94
β-strand	271	1	91
β-strand	272	1	94
α-helix	273-276	4
α-helix	279-282	4
α-helix	283-293	11
β-strand	295-301	7	91
α-helix	306-310	5
α-helix	313-315	3
β-strand	320-323	4	91
α-helix	331-339	9
β-strand	348-351	4	90
β-strand	357	1	95
β-strand	362-364	3	89
β-strand	371-372	2	89
α-helix	373-375	3
β-strand	386-393	8	89
β-strand	394	1	95
β-strand	404-410	7	90
β-strand	417-421	5	90

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A, C, E, G	protein	599	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B, D, F, H	protein	456	Homo sapiens	P26012 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6OM1_1 Integrin alpha-V (chains A, C, E, G)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSGCPPSFGYSMKGATDIDKNGY
PDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCL
KADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELI
AYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLTGGL

Sequence of entity 2 (B, D, F, H), FASTA

>6OM1_2 Integrin beta-8 (chains B, D, F, H)
EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYP
SVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNN
IEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPH
GYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLV
MTDQTSHLALDSKLAGIVCPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFA
VQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFN
ITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIH
IHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	20
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Water and common crystallization additives (MES, EDO) 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
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
8XEL 2.8 Å, Cryo-EM structure of integrin ITGAV/ITGB3 complex, conformation 3

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