4UM8: Alpha V beta 6

Crystal structure of alpha V beta 6. Determined by X-ray diffraction at 2.85 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 16,497
Mol. weight: 334.02 kDa
Ligands: NI, CA, CAC, MG
Released: 12 Nov 2014

Explore 4UM8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UM8 contains 67 α-helices and 173 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: 15 helices, 55 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
α-helix	70	1
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	160-163	4	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	279-282	4	10
β-strand	293-297	5	10
β-strand	301-303	3	11
β-strand	309-311	3	11
β-strand	314-320	7	10
α-helix	321	1
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	378	1	13
β-strand	383	1	13
β-strand	389-392	4	12
β-strand	407-412	6	2
β-strand	421-426	6	2
α-helix	427-429	3
β-strand	431-435	5	2
α-helix	436	1
β-strand	437	1	1
α-helix	438-439	2
β-strand	440-443	4	14
β-strand	446-450	5	15
β-strand	453-454	2	16
β-strand	472-479	8	15
β-strand	481-483	3	14
β-strand	490-499	10	17
β-strand	511-513	3	15
β-strand	520-528	9	17
β-strand	529	1	14
α-helix	532-533	2
β-strand	534-542	9	15
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	17
β-strand	577-578	2	14
β-strand	585-590	6	17
β-strand	591-592	2	16

Chain B: 19 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
β-strand	25	1	18
β-strand	26-27	2	19
β-strand	43	1	18
α-helix	45-51	7
β-strand	58-59	2	19
β-strand	64-69	6	20
α-helix	71-74	4
α-helix	81-83	3
β-strand	87-88	2	21
β-strand	91-96	6	20
β-strand	101-108	8	21
β-strand	116-123	8	22
α-helix	126-128	3
α-helix	129-132	4
α-helix	135-137	3
α-helix	138-146	9
β-strand	153-160	8	22
α-helix	173-177	5
α-helix	188-190	3
β-strand	193-200	8	22
α-helix	203-212	10
β-strand	223	1	23
α-helix	225-234	10
α-helix	236-239	4
β-strand	246-253	8	22
β-strand	257	1	23
α-helix	260-264	5
β-strand	270	1	24
β-strand	278	1	25
β-strand	283	1	22
β-strand	284	1	25
β-strand	290	1	24
α-helix	291-294	4
α-helix	295-304	10
β-strand	307-313	7	22
α-helix	315-325	11
β-strand	332-335	4	22
α-helix	343-354	12
β-strand	358-359	2	26
β-strand	360-363	4	20
β-strand	370-377	8	21
β-strand	381-384	4	21
β-strand	388-389	2	26
β-strand	398-405	8	21
β-strand	414-420	7	20
β-strand	427-433	7	20
α-helix	438-440	3

Chain C: 16 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	9-12	4	28
β-strand	22-26	5	29
β-strand	35-40	6	29
β-strand	55-60	6	29
β-strand	67-69	3	29
α-helix	70	1
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	168-173	6	33
α-helix	176-179	4
β-strand	181	1	34
β-strand	182-187	6	33
α-helix	188-193	6
β-strand	208-209	2	33
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	34
β-strand	226-229	4	35
α-helix	237	1
β-strand	238-243	6	35
α-helix	246-249	4
β-strand	252-256	5	35
β-strand	263-268	6	35
β-strand	279-283	5	36
β-strand	292-297	6	36
β-strand	301-303	3	37
β-strand	309-311	3	37
β-strand	314-320	7	36
α-helix	321	1
β-strand	326-332	7	36
β-strand	343-348	6	38
β-strand	357-362	6	38
α-helix	367-369	3
β-strand	372-376	5	38
β-strand	378	1	39
β-strand	383	1	39
β-strand	389-392	4	38
β-strand	407-412	6	28
β-strand	421-426	6	28
α-helix	427-429	3
β-strand	431-435	5	28
α-helix	436	1
β-strand	437	1	27
α-helix	438-439	2
β-strand	440-443	4	40
β-strand	446-450	5	41
β-strand	453-454	2	42
β-strand	462	1	43
β-strand	469	1	43
β-strand	472-479	8	41
β-strand	481-483	3	40
β-strand	490-499	10	44
α-helix	507-509	3
β-strand	511-513	3	41
β-strand	520-528	9	44
β-strand	529	1	40
α-helix	532-533	2
β-strand	534-542	9	41
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	44
β-strand	577-578	2	40
β-strand	585-590	6	44
β-strand	591-592	2	42

Chain D: 17 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
β-strand	26-27	2	45
β-strand	42	1	45
β-strand	58-59	2	45
β-strand	64-69	6	46
α-helix	71-74	4
α-helix	81-83	3
β-strand	87-88	2	47
β-strand	91-96	6	46
β-strand	98	1	48
β-strand	100	1	48
β-strand	101-108	8	47
β-strand	116-123	8	49
β-strand	125	1	50
α-helix	126-128	3
α-helix	129-135	7
α-helix	139-149	11
β-strand	153-160	8	49
α-helix	173-177	5
α-helix	188-190	3
β-strand	193-200	8	49
α-helix	203-212	10
β-strand	217	1	50
β-strand	223	1	51
α-helix	225-234	10
α-helix	236-239	4
β-strand	246-253	8	49
β-strand	257	1	51
α-helix	260-266	7
β-strand	270	1	52
β-strand	278	1	53
β-strand	283	1	49
β-strand	284	1	53
β-strand	290	1	52
α-helix	291-294	4
α-helix	295-304	10
β-strand	307-313	7	49
α-helix	318-325	8
β-strand	332-335	4	49
α-helix	343-354	12
β-strand	358-359	2	54
β-strand	360-363	4	46
β-strand	370-376	7	47
β-strand	383-384	2	47
β-strand	388-389	2	54
β-strand	398-405	8	47
β-strand	414-420	7	46
β-strand	427-433	7	46
α-helix	438-440	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A, C	protein	681	HOMO SAPIENS	P06756 (AlphaFold model)
Integrin beta-6	B, D	protein	788	HOMO SAPIENS	P18564 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4UM8_1 INTEGRIN ALPHA-V (chains A, C)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDTGGLE
VLFQGPGENAQLEKELQALEKENAQLEWELQALEKELAQTTGWRGGHVVEGLAGELEQLR
ARLEHHPQGQREPAGHHHHHH

Sequence of entity 2 (B, D), FASTA

>4UM8_2 INTEGRIN BETA-6 (chains B, D)
MGIELLCLFFLFLGRNDHVQGGCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCD
TPANLLAKGCQLNFIENPVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQT
LQVHVRQTEDYPVDLYYLMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEK
PVSPFVKTTPEEIANPCSSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPE
GGFDAIMQAAVCKEKIGWRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNE
YSMSTVLEYPTIGQLIDKLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNI
LQLIISAYEELRSEVELEVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVT
VNIPHCERRSRHIIIKPVGLGDALELLVSPECNCDCQKEVEVNSSKCHHGNGSFQCGVCA
CHPGHMGPRCECGEDMLSTDSCKEAPDHPSCSGRGDCYCGQCICHLSPYGNIYGPYCQCD
NFSCVRHKGLLCGGNGDCDCGECVCRSGWTGEYCNCTTSTDSCVSEDGVLCSGRGDCVCG
KCVCTNPGASGPTCERCPTCGDPCNSKRSCIECHLSAAGQAREECVDKCKLAGATISEEE
DFSKDGSVSCSLQGENECLITFLITTDNEGKTIIHSINEKDCPKPPNIPMIMLGVSLAIL
LIGVVLLCIWKLLVSFHDRKEVAKFEAERSKAKWQTGTNPLYRGSTSTFKNVTYKHREKQ
KVDLSTDC

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1
CA	Calcium ion	Ca	10
CAC	Cacodylate ion	C2 H6 As O2	2
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (CL, SO4) are not listed.

Primary citation

Structural Determinants of Integrin Beta-Subunit Specificity for Latent Tgf-Beta. Dong, X., Hudson, N.E., Lu, C. et al. Nat Struct Mol Biol (2014) 21:1091. DOI 10.1038/NSMB.2905 · 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

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