6MSL: Integrin AlphaVBeta3 ectodomain

Integrin AlphaVBeta3 ectodomain bound to EETI-II 2.5D. Determined by X-ray diffraction at 3.1 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Ecballium elaterium
Chains: 3
Atoms: 13,129
Mol. weight: 193.66 kDa
Ligands: MN, NAG
Released: 23 Oct 2019

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

Secondary structure: helices and β-sheets

6MSL contains 39 α-helices and 137 β-strands across 2 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: 12 helices, 88 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	8	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	97-100	4	6
β-strand	105-109	5	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	215-217	3
β-strand	222	1	8
β-strand	225-229	5	9
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	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
α-helix	395-397	3
β-strand	407-412	6	2
β-strand	421-426	6	2
β-strand	431-435	5	2
α-helix	436	1
β-strand	437	1	1
α-helix	438-439	2
β-strand	440-441	2	14
β-strand	442-449	8	15
β-strand	453-454	2	16
β-strand	461	1	17
β-strand	470	1	17
β-strand	472-474	3	18
β-strand	475-482	8	15
β-strand	490-499	10	19
β-strand	511-513	3	18
β-strand	520-528	9	19
β-strand	529	1	15
β-strand	534	1	15
β-strand	539-542	4	18
β-strand	555-563	9	19
β-strand	577-578	2	14
β-strand	585-590	6	19
β-strand	591-592	2	16
β-strand	606-611	6	20
β-strand	616-618	3	21
β-strand	623-633	11	20
β-strand	638	1	22
β-strand	641-646	6	23
β-strand	652-656	5	20
β-strand	668-671	4	23
β-strand	678-684	7	23
β-strand	687	1	22
β-strand	691-701	11	20
β-strand	711-712	2	24
β-strand	714-718	5	23
β-strand	726	1	23
α-helix	727-729	3
β-strand	730	1	23
β-strand	733-734	2	24
β-strand	735-737	3	21
β-strand	742-749	8	25
β-strand	752-755	4	26
α-helix	757	1
β-strand	775-784	10	25
β-strand	790	1	27
β-strand	792-802	11	26
β-strand	807	1	26
β-strand	809-817	9	25
β-strand	820-824	5	26
β-strand	869-872	4	26
β-strand	878-886	9	26
β-strand	889	1	27
β-strand	894-903	10	25
α-helix	905-908	4
β-strand	917-930	14	26
β-strand	941-953	13	26

Chain B: 27 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	13-17	5
β-strand	23	1	28
β-strand	25-26	2	29
β-strand	40	1	28
α-helix	43-46	4
β-strand	54-55	2	29
β-strand	60-65	6	30
α-helix	67-70	4
β-strand	72	1	31
β-strand	83-84	2	32
β-strand	87-92	6	30
β-strand	97-105	9	32
β-strand	108	1	31
β-strand	112-119	8	33
α-helix	122-127	6
α-helix	134-142	9
β-strand	149-156	8	33
α-helix	170-172	3
α-helix	179-181	3
β-strand	185	1	34
β-strand	190-197	8	33
α-helix	200-208	9
β-strand	213	1	34
α-helix	223-231	9
α-helix	233-236	4
α-helix	238-239	2
β-strand	243-250	8	33
α-helix	259-263	5
α-helix	267-269	3
β-strand	275	1	35
β-strand	280	1	33
β-strand	281	1	35
α-helix	288-291	4
α-helix	292-301	10
β-strand	305-310	6	33
α-helix	312-322	11
β-strand	329-332	4	33
α-helix	343-352	10
β-strand	354-356	3	36
β-strand	357-360	4	30
β-strand	366-373	8	32
β-strand	380-381	2	32
β-strand	385-387	3	36
β-strand	394-403	10	32
α-helix	411	1
β-strand	412-418	7	30
β-strand	425-431	7	30
α-helix	442-443	2
β-strand	447	1	37
β-strand	453	1	37
β-strand	462	1	37
β-strand	530	1	38
β-strand	535	1	38
α-helix	536-538	3
β-strand	540-543	4	39
β-strand	546-549	4	39
α-helix	550	1
β-strand	553-554	2	40
β-strand	560-561	2	40
β-strand	568	1	41
β-strand	574	1	41
α-helix	575-577	3
β-strand	579-582	4	42
β-strand	585-588	4	42
β-strand	594	1	43
β-strand	600	1	43
α-helix	605-606	2
α-helix	608-619	12
α-helix	624-627	4
α-helix	631-634	4
β-strand	639-641	3	44
β-strand	652-658	7	44
β-strand	664-670	7	44
β-strand	678-681	4	44
β-strand	686	1	44

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)
Cystine Knot Protein 2.5D	C	protein	32	Ecballium elaterium	P12071 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MSL_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

>6MSL_2 Integrin beta-3 (chains B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRP
SQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHG
QCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEK
CPTCPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCTYKNE
DDCVVRFQYYEDSSGKSILYVVEEPECPKGPDILV

Sequence of entity 3 (C), FASTA

>6MSL_3 Cystine Knot Protein 2.5D (chains C)
CPQGRGDWAPTSCKQDSDCLAGCVCGPNGFCG

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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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