8XEL: Integrin ITGAV/ITGB3 complex, conformation 3

Cryo-EM structure of integrin ITGAV/ITGB3 complex, conformation 3. Determined by electron microscopy at 2.8 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,282
Mol. weight: 203.31 kDa
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

8XEL contains 41 α-helices and 84 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: 16 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
α-helix	38	1
β-strand	39-42	4	2
β-strand	52-56	5	3
β-strand	65-70	6	3
β-strand	85-90	6	3
β-strand	97-99	3	3
β-strand	109-111	3	4
β-strand	114-115	2	4
β-strand	117-118	2	5
β-strand	127-131	5	6
β-strand	134-139	6	6
β-strand	143-144	2	5
β-strand	153	1	5
β-strand	157-161	5	6
β-strand	166-169	4	6
β-strand	190-193	4	7
β-strand	198-203	6	7
α-helix	206-209	4
β-strand	211	1	8
β-strand	212-217	6	7
α-helix	218-224	7
β-strand	238-239	2	7
α-helix	240-242	3
α-helix	245-247	3
β-strand	252	1	8
β-strand	255-259	5	9
α-helix	267	1
β-strand	268-273	6	9
α-helix	276-279	4
β-strand	282-286	5	9
β-strand	293-298	6	9
β-strand	309-313	5	10
β-strand	322-327	6	10
β-strand	331-333	3	11
β-strand	339-341	3	11
β-strand	344-350	7	10
β-strand	356-362	7	10
β-strand	374-378	5	12
β-strand	387-392	6	12
α-helix	397-399	3
β-strand	402-406	5	12
β-strand	408-409	2	13
β-strand	412-413	2	13
β-strand	419-422	4	12
β-strand	437-442	6	2
β-strand	451-456	6	2
α-helix	457-459	3
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	14
β-strand	472-479	8	15
β-strand	483	1	16
β-strand	489-491	3	15
β-strand	500-512	13	15
β-strand	520-529	10	17
α-helix	531-533	3
α-helix	537-539	3
β-strand	541-543	3	15
β-strand	548	1	15
β-strand	550-558	9	17
β-strand	564-572	9	15
α-helix	573-574	2
α-helix	584	1
β-strand	585-593	9	17
α-helix	595-598	4
β-strand	607-608	2	14
β-strand	615-620	6	17
β-strand	621	1	16

Chain B: 25 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
α-helix	39-45	7
β-strand	50-51	2	18
α-helix	58	1
β-strand	64-65	2	18
α-helix	67-72	6
α-helix	77-79	3
β-strand	86-91	6	19
α-helix	93-96	4
α-helix	103-105	3
β-strand	109	1	20
β-strand	113-118	6	19
β-strand	123-131	9	20
β-strand	138-145	8	21
α-helix	148-150	3
α-helix	151-156	6
α-helix	160-168	9
β-strand	175-182	8	21
α-helix	197-200	4
α-helix	204-206	3
α-helix	211-213	3
β-strand	216-223	8	21
α-helix	227-234	8
β-strand	246	1	22
α-helix	248-257	10
α-helix	259-262	4
β-strand	269-276	8	21
β-strand	280	1	22
α-helix	285-289	5
α-helix	294-295	2
β-strand	301	1	23
β-strand	306	1	21
β-strand	307	1	23
α-helix	314-317	4
α-helix	318-327	10
β-strand	330-337	8	21
α-helix	338-340	3
α-helix	341-348	8
β-strand	354-359	6	21
α-helix	366-378	13
β-strand	380-382	3	24
β-strand	383-386	4	19
β-strand	392-398	7	20
β-strand	406-407	2	20
β-strand	411-413	3	24
β-strand	420-429	10	20
β-strand	437-444	8	19
β-strand	451-457	7	19
α-helix	462-466	5
β-strand	479-480	2	25
α-helix	481	1
β-strand	487-488	2	25
β-strand	492-493	2	26
β-strand	499-500	2	26

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

>8XEL_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

>8XEL_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, conformation 3. 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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