8XEI: Integrin ITGAV/ITGB3 complex, conformation 1

Cryo-EM structure of integrin ITGAV/ITGB3 complex, conformation 1. Determined by electron microscopy at 2.9 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,391
Mol. weight: 203.31 kDa
Released: 18 Dec 2024

Explore 8XEI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XEI contains 54 α-helices and 132 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: 19 helices, 84 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
β-strand	39-42	4	2
β-strand	52-56	5	3
β-strand	65-70	6	3
β-strand	84	1	4
β-strand	85-90	6	3
β-strand	97-99	3	3
β-strand	109-111	3	5
β-strand	114-115	2	5
β-strand	117-118	2	6
β-strand	124	1	4
β-strand	127-131	5	7
β-strand	134-139	6	7
β-strand	143-144	2	6
β-strand	153-154	2	6
β-strand	157-162	6	7
β-strand	165-169	5	7
β-strand	190-193	4	8
β-strand	198-203	6	8
α-helix	206-209	4
β-strand	211	1	9
β-strand	212-217	6	8
α-helix	218-223	6
β-strand	238-239	2	8
α-helix	245-247	3
β-strand	252	1	9
β-strand	255-259	5	10
α-helix	267	1
β-strand	268-273	6	10
α-helix	276-279	4
β-strand	282-286	5	10
β-strand	293-298	6	10
β-strand	309-313	5	11
β-strand	322-327	6	11
β-strand	331-333	3	12
α-helix	335-337	3
β-strand	339-341	3	12
β-strand	344-350	7	11
β-strand	356-362	7	11
β-strand	374-378	5	13
β-strand	387-392	6	13
β-strand	402-406	5	13
β-strand	408-409	2	14
β-strand	412-413	2	14
β-strand	419-422	4	13
β-strand	437-442	6	2
β-strand	451-455	5	2
β-strand	461-465	5	2
α-helix	466	1
β-strand	467	1	1
α-helix	468-469	2
β-strand	470-471	2	15
β-strand	472-478	7	16
β-strand	483-484	2	17
β-strand	491-492	2	18
β-strand	499-500	2	18
β-strand	502-512	11	16
β-strand	520-528	9	19
α-helix	537-539	3
β-strand	541-543	3	16
β-strand	550-558	9	19
β-strand	564-572	9	16
α-helix	573-574	2
α-helix	575-577	3
α-helix	584	1
β-strand	585-593	9	19
α-helix	595-598	4
β-strand	607-608	2	15
β-strand	615-620	6	19
β-strand	621-622	2	17
β-strand	636-641	6	20
β-strand	646-648	3	21
β-strand	656-663	8	20
β-strand	668	1	22
β-strand	671-676	6	21
β-strand	682-686	5	20
α-helix	694-695	2
β-strand	698-703	6	21
β-strand	706-714	9	21
β-strand	717	1	22
α-helix	718	1
β-strand	722-730	9	20
β-strand	740-748	9	21
β-strand	756	1	21
α-helix	757-759	3
β-strand	760-767	8	21
β-strand	772-779	8	23
β-strand	782-784	3	24
α-helix	787	1
α-helix	799-802	4
β-strand	805-814	10	23
β-strand	820	1	25
β-strand	822-832	11	24
β-strand	833	1	26
β-strand	836	1	26
β-strand	839-847	9	23
β-strand	850-854	5	24
β-strand	908-916	9	24
β-strand	919	1	25
β-strand	924-933	10	23
α-helix	935-944	10
β-strand	948-960	13	24
β-strand	972-982	11	24

Chain B: 35 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	30-34	5
α-helix	39-43	5
β-strand	50-52	3	27
α-helix	58	1
β-strand	64-65	2	27
α-helix	67-70	4
α-helix	71-73	3
α-helix	77-79	3
β-strand	80-81	2	27
β-strand	86-91	6	28
α-helix	93-96	4
β-strand	109-110	2	29
β-strand	113-118	6	28
β-strand	123-131	9	29
β-strand	138-145	8	30
α-helix	148-150	3
α-helix	151-156	6
α-helix	157-159	3
α-helix	160-168	9
β-strand	175-182	8	30
α-helix	196-200	5
α-helix	202-204	3
α-helix	211-213	3
β-strand	216-223	8	30
α-helix	227-234	8
β-strand	246	1	31
α-helix	248-257	10
α-helix	259-262	4
β-strand	269-276	8	30
β-strand	280	1	31
α-helix	286-289	4
α-helix	294-295	2
β-strand	301	1	32
β-strand	306	1	30
β-strand	307	1	32
α-helix	308-311	4
α-helix	314-317	4
α-helix	318-328	11
β-strand	331-337	7	30
α-helix	338-340	3
α-helix	341-349	9
β-strand	355-359	5	30
α-helix	360	1
α-helix	366-378	13
β-strand	380-382	3	33
β-strand	383-386	4	28
β-strand	392-399	8	29
α-helix	401-403	3
β-strand	405-407	3	29
β-strand	411-413	3	33
β-strand	420-429	10	29
β-strand	437-444	8	28
β-strand	451-457	7	28
α-helix	462-466	5
β-strand	468-469	2	34
β-strand	479-481	3	34
β-strand	486-488	3	34
β-strand	492-493	2	35
α-helix	495-497	3
β-strand	499-500	2	35
β-strand	525-528	4	36
β-strand	531-534	4	36
β-strand	542-543	2	37
β-strand	549-550	2	37
β-strand	566-569	4	38
β-strand	572-575	4	38
β-strand	580	1	39
β-strand	586	1	39
α-helix	591-593	3
β-strand	594	1	40
β-strand	600	1	40
α-helix	601-603	3
β-strand	605-606	2	41
β-strand	613-614	2	41
α-helix	631-632	2
α-helix	633-645	13
α-helix	650-654	5
α-helix	657-660	4
β-strand	664-668	5	42
β-strand	681-684	4	42
β-strand	690-693	4	42
β-strand	696-697	2	42
β-strand	703-708	6	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A	protein	1048	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-3	B	protein	788	Homo sapiens	P05106 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8XEI_1 Integrin alpha-V (chains A)
MAFPPRRRLRLGPRGLPLLLSGLLLPLCRAFNLDVDSPAEYSGPEGSYFGFAVDFFVPSA
SSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKS
HQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDAD
GQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLAT
RTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGE
QMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTK
LNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQI
LEGQWAARSMPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVY
PSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKQKGAIRR
ALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAAD
TTGLQPILNQFTPANISRQAHILLDCGEDNVCKPKLEVSVDSDQKKIYIGDDNPLTLIVK
AQNQGEGAYEAELIVSIPLQADFIGVVRNNEALARLSCAFKTENQTRQVVCDLGNPMKAG
TQLLAGLRFSVHQQSEMDTSVKFDLQIQSSNLFDKVSPVVSHKVDLAVLAAVEIRGVSSP
DHVFLPIPNWEHKENPETEEDVGPVVQHIYELRNNGPSSFSKAMLHLQWPYKYNNNTLLY
ILHYDIDGPMNCTSDMEINPLRIKISSLQTTEKNDTVAGQGERDHLITKRDLALSEGDIH
TLGCGVAQCLKIVCQVGRLDRGKSAILYVKSLLWTETFMNKENQNHSYSLKSSASFNVIE
FPYKNLPIEDITNSTLVTTNVTWGIQPAPMPVPVWVIILAVLAGLLLLAVLVFVMYRMGF
FKRVRPPQEEQEREQLQPHENGEGNSET

Sequence of entity 2 (B), FASTA

>8XEI_2 Integrin beta-3 (chains B)
MRARPRPRPLWATVLALGALAGVGVGGPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLG
SPRCDLKENLLKDNCAPESIEFPVSEARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRP
DDSKNFSIQVRQVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFG
AFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSR
NRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCH
VGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVLS
MDSSNVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDT
VSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGT
FECGVCRCGPGWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFG
KITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLL
CSGRGKCECGSCVCIQPGSYGDTCEKCPTCPDACTFKKECVECKKFDRGALHDENTCNRY
CRDEIESVKELKDTGKDAVNCTYKNEDDCVVRFQYYEDSSGKSILYVVEEPECPKGPDIL
VVLLSVMGAILLIGLAALLIWKLLITIHDRKEFAKFEEERARAKWDTANNPLYKEATSTF
TNITYRGT

Primary citation

Cryo-EM structure of integrin ITGAV/ITGB3 complex. Xi, Z. 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

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