9JEI: Integrin alpha-v beta-3

Integrin alpha-v beta-3 in complex with Echistatin. Determined by electron microscopy at 3.16 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organisms: Homo sapiens, Echis carinatus
Chains: 3
Atoms: 9,956
Mol. weight: 243.72 kDa
Ligands: CA, NAG, MG
Released: 10 Sept 2025

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

Secondary structure: helices and β-sheets

9JEI contains 39 α-helices and 107 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: 11 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	9-12	4	2
β-strand	23-26	4	3
β-strand	35-40	6	3
β-strand	54	1	4
β-strand	55-60	6	3
β-strand	67-69	3	3
β-strand	79-81	3	5
β-strand	84-85	2	5
β-strand	87-88	2	6
β-strand	94	1	4
β-strand	97-100	4	7
β-strand	105-109	5	7
β-strand	113-114	2	6
β-strand	123	1	6
β-strand	127-131	5	7
β-strand	136-139	4	7
β-strand	160-164	5	8
β-strand	168-173	6	8
α-helix	176-179	4
β-strand	181	1	9
β-strand	182-187	6	8
α-helix	188-193	6
α-helix	202-204	3
β-strand	208-209	2	8
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	9
β-strand	225-229	5	10
α-helix	237	1
β-strand	238-243	6	10
α-helix	246-249	4
β-strand	252-256	5	10
β-strand	263-268	6	10
β-strand	280-283	4	11
β-strand	292-297	6	11
β-strand	301-303	3	12
β-strand	309-311	3	12
β-strand	314-320	7	11
β-strand	326-332	7	11
β-strand	343-348	6	13
β-strand	357-362	6	13
α-helix	367-369	3
β-strand	372-377	6	13
β-strand	378	1	14
β-strand	383	1	14
β-strand	390-392	3	13
β-strand	407-410	4	2
β-strand	422-426	5	2
β-strand	431-435	5	2
β-strand	437	1	1
α-helix	438-439	2
β-strand	440-441	2	15
β-strand	442-449	8	16
β-strand	453-454	2	17
β-strand	472-482	11	16
β-strand	490-499	10	18
β-strand	511-513	3	16
β-strand	520-528	9	18
β-strand	529	1	16
β-strand	536-542	7	16
α-helix	554	1
β-strand	555-563	9	18
β-strand	577-578	2	15
β-strand	585-590	6	18
β-strand	591-592	2	17
β-strand	606-611	6	19
β-strand	616-617	2	20
β-strand	623-633	11	19
β-strand	638	1	21
β-strand	641-645	5	22
β-strand	652-656	5	19
β-strand	668-671	4	22
β-strand	678-684	7	22
β-strand	687	1	21
β-strand	691-701	11	19
β-strand	711-712	2	23
β-strand	715-718	4	22
β-strand	726	1	22
α-helix	727-729	3
β-strand	730	1	22
β-strand	733-734	2	23
β-strand	735-736	2	20

Chain B: 24 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	13-19	7
β-strand	24-26	3	24
α-helix	32	1
β-strand	33	1	25
β-strand	35	1	25
β-strand	38-39	2	24
α-helix	41-46	6
α-helix	51-53	3
β-strand	54-55	2	24
α-helix	57-59	3
β-strand	60-65	6	26
α-helix	67-69	3
β-strand	83-84	2	27
β-strand	87-92	6	26
β-strand	96-106	11	27
α-helix	109-111	3
β-strand	112-119	8	28
α-helix	122-124	3
α-helix	128-145	18
β-strand	149-156	8	28
α-helix	170-172	3
α-helix	176-178	3
α-helix	185-187	3
β-strand	190	1	28
β-strand	191	1	29
β-strand	194-197	4	28
α-helix	200-208	9
β-strand	220	1	30
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	28
β-strand	254	1	30
α-helix	259-261	3
β-strand	275	1	31
β-strand	280	1	29
β-strand	281	1	31
α-helix	282-285	4
α-helix	288-291	4
α-helix	292-302	11
β-strand	304-310	7	28
α-helix	312-314	3
α-helix	315-324	10
β-strand	329-332	4	28
α-helix	338-349	12
β-strand	353-356	4	32
β-strand	357-360	4	26
β-strand	366-373	8	27
β-strand	379-381	3	27
β-strand	385-389	5	32
β-strand	393-403	11	27
β-strand	412	1	26
β-strand	415-418	4	26
β-strand	425-431	7	26
α-helix	437-440	4
β-strand	455-456	2	33
β-strand	459-460	2	33

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	19-21	3	34
α-helix	22-24	3
β-strand	30-31	2	34
α-helix	40-42	3
α-helix	43-45	3

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)
Metalloproteinase	C	protein	49	Echis carinatus	E9JGH0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JEI_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

>9JEI_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

>9JEI_3 Metalloproteinase (chains C)
ECESGPCCRNCKFLKEGTICKRARGDDMDDYCNGKTCDCPRNPHKGPAT

Ligands and cofactors

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

Primary citation

Integrin alpha-v beta-3 in complex with Echistatin. Wang, Y.T., Chuang, W.J. To be published.

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

Browse structure collections

About this viewer

MolViewer shows 9JEI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.