9IUJ: Integrin alpha-v beta-3

Integrin alpha-v beta-3 in complex with rhodostomin. Determined by electron microscopy at 2.78 Å resolution. Released 30 Jul 2025.

Method: Electron microscopy
Resolution: 2.78 Å
Organisms: Homo sapiens, Calloselasma rhodostoma
Chains: 3
Atoms: 10,072
Mol. weight: 245.63 kDa
Ligands: MG, NAG, CA
Released: 30 Jul 2025

Explore 9IUJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IUJ contains 38 α-helices and 109 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: 12 helices, 71 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	67-70	4	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
α-helix	202-204	3
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	372-376	5	12
β-strand	378-379	2	13
β-strand	382-383	2	13
β-strand	389-392	4	12
β-strand	407-410	4	2
β-strand	422-426	5	2
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	446-449	4	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
β-strand	534-542	9	15
α-helix	554	1
β-strand	555-563	9	17
β-strand	577-578	2	14
β-strand	585-590	6	17
β-strand	591-592	2	16
β-strand	606-611	6	18
β-strand	616-617	2	19
β-strand	623-633	11	18
β-strand	638	1	20
β-strand	641-645	5	21
β-strand	652-656	5	18
β-strand	668-671	4	21
β-strand	678-684	7	21
β-strand	687	1	20
β-strand	691-701	11	18
β-strand	711-712	2	22
β-strand	715-718	4	21
β-strand	726	1	21
α-helix	727-729	3
β-strand	730	1	21
β-strand	733-734	2	22
β-strand	735-736	2	19

Chain B: 23 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	13-19	7
β-strand	24-26	3	23
α-helix	32	1
β-strand	33	1	24
β-strand	35	1	24
β-strand	38-39	2	23
α-helix	41-46	6
α-helix	51-53	3
β-strand	54-55	2	23
α-helix	57-59	3
β-strand	60-65	6	25
α-helix	67-70	4
β-strand	83-84	2	26
β-strand	87-92	6	25
β-strand	96-105	10	26
α-helix	109-110	2
β-strand	111-119	9	27
α-helix	122-124	3
α-helix	128-145	18
β-strand	148-156	9	27
α-helix	171-174	4
α-helix	176-178	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
β-strand	220	1	29
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	27
β-strand	254	1	29
α-helix	267-269	3
β-strand	275	1	30
β-strand	280	1	27
β-strand	281	1	30
α-helix	288-291	4
α-helix	292-302	11
β-strand	304-310	7	27
α-helix	312-314	3
α-helix	315-324	10
β-strand	329-332	4	27
α-helix	338-349	12
β-strand	357-360	4	25
β-strand	366-373	8	26
β-strand	379-381	3	26
β-strand	394-403	10	26
β-strand	412	1	25
β-strand	415-418	4	25
β-strand	425-431	7	25
α-helix	436-440	5
β-strand	442	1	31
β-strand	455-456	2	31
β-strand	459-460	2	31

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	32
β-strand	21	1	32
α-helix	22	1
β-strand	33-34	2	33
β-strand	37-38	2	33
α-helix	39-40	2
β-strand	46	1	34
α-helix	53-54	2
β-strand	55	1	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V,Integrin alpha-V,Uncharacterized protein DKFZp686C11235	A	protein	1184	Homo sapiens	P06756 (AlphaFold model), Q6MZV7 (AlphaFold model)
Integrin beta-3,Integrin beta-3,Uncharacterized protein DKFZp686C11235	B	protein	919	Homo sapiens	P05106 (AlphaFold model), Q6MZV7 (AlphaFold model)
Disintegrin rhodostomin	C	protein	68	Calloselasma rhodostoma	P30403 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9IUJ_1 Integrin alpha-V,Integrin alpha-V,Uncharacterized protein DKFZp686C11235 (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPDKT
HTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVE
VHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQP
REPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGS
FFLTSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 2 (B), FASTA

>9IUJ_2 Integrin beta-3,Integrin beta-3,Uncharacterized protein DKFZp686C11235 (chains B)
GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSE
ARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDL
SYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDM
KTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRN
DASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLS
QKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVR
DLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVG
FKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRP
SQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHG
QCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEK
CPTCPDACTFKKECVECKKFDRGALHDENTCNRYCRDEIESVKELKDTGKDAVNCTYKNE
DDCVVRFQYYEDSSGKSILYVVEEPECPKGPDDKTHTCPPCPAPELLGGPSVFLFPPKPK
DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTV
LHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLYCL
VKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM
HEALHNHYTQKSLSLSPGK

Sequence of entity 3 (C), FASTA

>9IUJ_3 Disintegrin rhodostomin (chains C)
GKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIPRGDMPDDRCTGQ
SADCPRYH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	7

Primary citation

Structural basis for the differential recognition of integrin alpha v beta 3 by rhodostomin and trimucrin. Wang, Y.T., Chang, Y.T., Huang, C.H. et al. Commun Biol (2026) 9. DOI 10.1038/s42003-026-10139-6 · 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
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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