4UM9: Alpha V beta 6 with peptide

Crystal structure of alpha V beta 6 with peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,049
Mol. weight: 250.39 kDa
Ligands: CA, MG, NAG, MAN
Released: 12 Nov 2014

Explore 4UM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UM9 contains 68 α-helices and 173 β-strands across 6 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: 14 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	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	127-132	6	6
β-strand	135-139	5	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	279-283	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
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	404-412	9	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	440-450	11	14
β-strand	453-454	2	15
β-strand	472-483	12	14
β-strand	490-499	10	16
β-strand	505	1	17
β-strand	507	1	17
β-strand	511-513	3	14
β-strand	518	1	14
β-strand	520-528	9	16
α-helix	532-533	2
β-strand	534-542	9	14
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	16
β-strand	577-578	2	14
β-strand	585-590	6	16
β-strand	591-592	2	15

Chain B: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
β-strand	25-26	2	18
β-strand	42-43	2	18
α-helix	45-51	7
β-strand	59	1	18
β-strand	64-69	6	19
α-helix	71-74	4
α-helix	81-83	3
β-strand	87-88	2	20
β-strand	91-96	6	19
β-strand	102-109	8	20
β-strand	116-123	8	21
α-helix	126-128	3
α-helix	129-134	6
α-helix	135-137	3
α-helix	138-149	12
β-strand	153-160	8	21
α-helix	173-177	5
α-helix	188-190	3
β-strand	193-200	8	21
α-helix	203-211	9
β-strand	223	1	22
α-helix	225-234	10
α-helix	236-239	4
β-strand	246-253	8	21
β-strand	257	1	22
α-helix	260-266	7
β-strand	270	1	23
α-helix	271-272	2
β-strand	278	1	24
β-strand	283	1	21
β-strand	284	1	24
β-strand	290	1	23
α-helix	291-294	4
α-helix	295-304	10
β-strand	307-313	7	21
α-helix	315-325	11
β-strand	332-335	4	21
α-helix	343-354	12
β-strand	358-359	2	25
β-strand	360-364	5	19
β-strand	370-376	7	20
β-strand	383-384	2	20
β-strand	388-389	2	25
β-strand	394	1	26
β-strand	396	1	26
β-strand	397-405	9	20
β-strand	414-420	7	19
β-strand	427-433	7	19
β-strand	455-458	4	27
β-strand	461-464	4	27

Chain C: 15 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	77-78	2
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	225-229	5	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
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	372-377	6	38
β-strand	378-379	2	39
β-strand	382-383	2	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	431-437	7	28
α-helix	438-439	2
β-strand	440-450	11	40
β-strand	453-454	2	41
β-strand	461-462	2	42
β-strand	469-470	2	42
β-strand	472-483	12	40
β-strand	490-498	9	43
β-strand	511-513	3	40
β-strand	520-528	9	43
α-helix	532-533	2
β-strand	534-542	9	40
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	43
α-helix	565-568	4
β-strand	577-578	2	40
α-helix	579	1
β-strand	585-590	6	43
β-strand	591-592	2	41

Chain D: 18 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	14-19	6
β-strand	25	1	44
β-strand	26-27	2	45
β-strand	43	1	44
α-helix	45-51	7
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	102-109	8	47
β-strand	116-123	8	48
α-helix	126-128	3
α-helix	129-135	7
α-helix	138-149	12
β-strand	153-160	8	48
α-helix	173-177	5
α-helix	188-190	3
β-strand	193-200	8	48
α-helix	203-211	9
β-strand	223	1	49
α-helix	225-234	10
α-helix	236-239	4
β-strand	246-253	8	48
β-strand	257	1	49
α-helix	260-266	7
β-strand	270	1	50
α-helix	271-272	2
β-strand	278	1	51
β-strand	283	1	48
β-strand	284	1	51
β-strand	290	1	50
α-helix	291-294	4
α-helix	295-304	10
β-strand	307-313	7	48
α-helix	315-327	13
β-strand	332-335	4	48
α-helix	343-354	12
β-strand	358-359	2	52
β-strand	360-364	5	46
β-strand	370-376	7	47
β-strand	382-384	3	47
β-strand	388-389	2	52
β-strand	394	1	53
β-strand	396	1	53
β-strand	397-405	9	47
β-strand	414-420	7	46
β-strand	427-433	7	46
β-strand	444	1	54
β-strand	456-458	3	54
β-strand	461-463	3	54

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	245-248	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V heavy chain	A, C	protein	604	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	483	Homo sapiens	P18564 (AlphaFold model)
Integrin beta-6	D	protein	483	Homo sapiens	P18564 (AlphaFold model)
Latency-associated peptide	E, F	protein	13	Homo sapiens	P10600 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4UM9_1 Integrin alpha-V heavy chain (chains A, C)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDTGGLE
VLFQ

Sequence of entity 2 (B), FASTA

>4UM9_2 Integrin beta-6 (chains B)
HVQGGCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIEN
PVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYY
LMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPC
SSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIG
WRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLID
KLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVEL
EVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKP
VGLGDALELLVSPECNCDCQKEVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCESRGLQT
LFQ

Sequence of entity 3 (D), FASTA

>4UM9_3 Integrin beta-6 (chains D)
HVQGGCALGGAETCEDCLLIGPQCAWCATENFTHPSGVGERCDTPANLLAKGCQLNFIEN
PVSQVEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYY
LMDLSASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPC
SSIPYFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIG
WRNDSLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLID
KLVQNNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVEL
EVLGDTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKP
VGLGDALELLVSPECNCDCQKEVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCESRGLQT
LFQ

Sequence of entity 4 (E, F), FASTA

>4UM9_4 Latency-associated peptide (chains E, F)
XHGRGDLGRLKKX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12
MG	Magnesium ion	Mg	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
MAN	alpha-D-mannopyranose	C6 H12 O6	1

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

Browse structure collections

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