6MSU: Integrin alphaVBeta3

Integrin alphaVBeta3 in complex with EETI-II 2.5F. Determined by X-ray diffraction at 3.11 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 3.11 Å
Organisms: Homo sapiens, Ecballium elaterium
Chains: 3
Atoms: 13,158
Mol. weight: 194.13 kDa
Ligands: NAG, MN
Released: 23 Oct 2019

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

Secondary structure: helices and β-sheets

6MSU contains 44 α-helices and 130 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: 17 helices, 79 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	9-12	4	1
β-strand	22-26	5	2
β-strand	35-40	6	2
β-strand	55-59	5	2
β-strand	67-69	3	2
β-strand	79	1	3
β-strand	85	1	3
β-strand	87-88	2	4
β-strand	97-101	5	5
β-strand	104-109	6	5
β-strand	113-114	2	4
β-strand	123	1	4
β-strand	127-132	6	5
β-strand	135-139	5	5
α-helix	152-154	3
β-strand	160-163	4	6
β-strand	168-173	6	6
α-helix	176-179	4
β-strand	181	1	7
β-strand	182-187	6	6
α-helix	188-193	6
β-strand	208-209	2	6
α-helix	215-217	3
β-strand	222	1	7
β-strand	225-229	5	8
α-helix	237	1
β-strand	238-243	6	8
α-helix	246-249	4
β-strand	252-256	5	8
β-strand	263-268	6	8
β-strand	279-283	5	9
β-strand	292-297	6	9
β-strand	301-303	3	10
β-strand	309-311	3	10
β-strand	314-320	7	9
β-strand	326-332	7	9
β-strand	343-348	6	11
β-strand	357-362	6	11
α-helix	367-369	3
β-strand	372-377	6	11
β-strand	378-379	2	12
β-strand	382-383	2	12
β-strand	389-392	4	11
β-strand	407-412	6	1
β-strand	421-426	6	1
β-strand	431-435	5	1
β-strand	440-441	2	13
β-strand	442-445	4	14
β-strand	448-449	2	14
β-strand	453-454	2	15
β-strand	471-482	12	14
β-strand	491-499	9	16
α-helix	501-503	3
α-helix	508-509	2
β-strand	511-513	3	14
β-strand	520-527	8	16
β-strand	534-542	9	14
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-560	6	16
β-strand	577-578	2	13
β-strand	585-590	6	16
β-strand	591-592	2	15
β-strand	606-611	6	17
β-strand	616-618	3	18
β-strand	625-633	9	17
β-strand	638	1	19
β-strand	642-646	5	18
β-strand	652-656	5	17
α-helix	664-665	2
β-strand	668-673	6	18
β-strand	676-682	7	18
β-strand	687	1	19
β-strand	691-700	10	17
β-strand	710-718	9	18
β-strand	726	1	18
α-helix	727-729	3
β-strand	730-737	8	18
β-strand	742-749	8	20
β-strand	752-755	4	21
α-helix	757	1
α-helix	769-772	4
β-strand	775-784	10	20
β-strand	790	1	22
β-strand	792-802	11	21
β-strand	807	1	21
β-strand	809-817	9	20
β-strand	820-824	5	21
β-strand	870-872	3	21
β-strand	878-886	9	21
β-strand	889	1	22
β-strand	894-903	10	20
α-helix	905-908	4
β-strand	918-930	13	21
β-strand	941-953	13	21

Chain B: 26 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	14-17	4
β-strand	25-26	2	23
β-strand	38	1	23
β-strand	54-55	2	23
β-strand	60-65	6	24
α-helix	67-70	4
β-strand	72	1	25
β-strand	83-84	2	26
β-strand	87-92	6	24
β-strand	97-105	9	26
β-strand	108	1	25
β-strand	112-119	8	27
α-helix	122-131	10
α-helix	134-142	9
β-strand	149-156	8	27
α-helix	170-172	3
β-strand	185	1	28
α-helix	186-187	2
β-strand	190-197	8	27
α-helix	200-208	9
β-strand	213	1	28
α-helix	223-231	9
α-helix	233-236	4
α-helix	238-239	2
β-strand	243-250	8	27
α-helix	259-263	5
α-helix	267-269	3
β-strand	275	1	29
β-strand	280	1	27
β-strand	281	1	29
α-helix	282-285	4
α-helix	288-291	4
α-helix	292-301	10
β-strand	305-310	6	27
α-helix	312-314	3
α-helix	315-322	8
β-strand	329-332	4	27
α-helix	345-351	7
β-strand	354-356	3	30
β-strand	357-360	4	24
β-strand	366-373	8	26
β-strand	379-381	3	26
β-strand	385-387	3	30
β-strand	394-403	10	26
β-strand	412-418	7	24
β-strand	425-431	7	24
β-strand	454	1	31
β-strand	461	1	31
α-helix	478-479	2
β-strand	502	1	32
β-strand	505	1	32
β-strand	517	1	33
β-strand	523	1	33
β-strand	530	1	34
β-strand	535	1	34
α-helix	536-538	3
β-strand	540-543	4	35
β-strand	546-549	4	35
β-strand	553-554	2	36
β-strand	560-561	2	36
β-strand	568	1	37
β-strand	574	1	37
α-helix	575-577	3
β-strand	579-582	4	38
β-strand	585-588	4	38
β-strand	594	1	39
β-strand	600	1	39
α-helix	605-606	2
α-helix	608-618	11
α-helix	624-627	4
α-helix	631-634	4
β-strand	639-642	4	40
β-strand	654-658	5	40
β-strand	664-668	5	40
β-strand	679-682	4	40
β-strand	686	1	40

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A	protein	967	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-3	B	protein	695	Homo sapiens	P05106 (AlphaFold model)
Engineered EETI-II 2.5F	C	protein	32	Ecballium elaterium	P12071 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MSU_1 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPAPM
PVPVWVI

Sequence of entity 2 (B), FASTA

>6MSU_2 Integrin beta-3 (chains B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRP
SQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHG
QCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEK
CPTCPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCTYKNE
DDCVVRFQYYEDSSGKSILYVVEEPECPKGPDILV

Sequence of entity 3 (C), FASTA

>6MSU_3 Engineered EETI-II 2.5F (chains C)
CPRPRGDNPPLTCKQDSDCLAGCVCGPNGFCG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
MN	Manganese (II) ion	Mn	8

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

Primary citation

Structural Basis of the Differential Binding of Engineered Knottins to Integrins alpha V beta 3 and alpha 5 beta 1. Van Agthoven, J.F., Shams, H., Cochran, F.V. et al. Structure (2019) 27:1443-1451.e6. DOI 10.1016/j.str.2019.06.011 · 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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