8XFG: Integrin alpha-V

Cryo-EM structure of integrin ITGAV, ITGB3 and CYCLO (RGDFK) complex, conformation 1. Determined by electron microscopy at 2.8 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,378
Mol. weight: 203.91 kDa
Ligands: A1LU7
Released: 18 Dec 2024

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

Secondary structure: helices and β-sheets

8XFG contains 38 α-helices and 102 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: 14 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	1
β-strand	52-56	5	2
β-strand	65-70	6	2
β-strand	85-90	6	2
β-strand	98-100	3	2
α-helix	107-108	2
β-strand	109	1	3
α-helix	110	1
β-strand	115	1	3
β-strand	117-118	2	4
β-strand	127-131	5	5
β-strand	134-139	6	5
β-strand	143-144	2	4
β-strand	153	1	4
β-strand	157-161	5	5
β-strand	166-169	4	5
β-strand	190-193	4	6
β-strand	199-203	5	6
α-helix	206-209	4
β-strand	211	1	7
β-strand	212-216	5	6
α-helix	218-223	6
β-strand	238-239	2	6
α-helix	240-242	3
α-helix	245-247	3
β-strand	252	1	7
β-strand	255-259	5	8
α-helix	267	1
β-strand	268-273	6	8
β-strand	282-286	5	8
β-strand	293-298	6	8
β-strand	309-313	5	9
β-strand	322-327	6	9
β-strand	331-333	3	10
β-strand	339-341	3	10
β-strand	343	1	11
β-strand	344-348	5	9
β-strand	359-362	4	9
β-strand	370	1	11
β-strand	373-378	6	12
β-strand	387-392	6	12
α-helix	397-399	3
β-strand	402-406	5	12
β-strand	419-422	4	12
α-helix	426-427	2
β-strand	437-442	6	1
β-strand	451-456	6	1
β-strand	461-465	5	1
α-helix	467-469	3
β-strand	470-471	2	13
β-strand	472-479	8	14
β-strand	483-485	3	15
β-strand	491-492	2	16
α-helix	493	1
β-strand	499-500	2	16
β-strand	503-512	10	14
β-strand	520-528	9	17
α-helix	537-539	3
β-strand	541-543	3	14
β-strand	550-558	9	17
β-strand	564-572	9	14
β-strand	585-593	9	17
α-helix	598-599	2
β-strand	607-608	2	13
β-strand	615-620	6	17
β-strand	621-623	3	15
β-strand	635-642	8	18
β-strand	646-647	2	19
β-strand	653-664	12	18
β-strand	668	1	20
β-strand	672-675	4	19
β-strand	676	1	21
β-strand	681-686	6	18
β-strand	697-698	2	19
β-strand	701	1	21
β-strand	708	1	21
β-strand	711-712	2	19
β-strand	717	1	20
β-strand	722-731	10	18
β-strand	740-747	8	19
β-strand	748	1	22
β-strand	756	1	22
α-helix	757-759	3
β-strand	760-766	7	19

Chain B: 24 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
α-helix	39-45	7
β-strand	50-51	2	23
β-strand	52	1	24
α-helix	57-58	2
β-strand	64-65	2	23
α-helix	67-72	6
α-helix	77-79	3
β-strand	80	1	24
α-helix	83-85	3
β-strand	87-91	5	25
α-helix	93-96	4
β-strand	113-118	6	25
β-strand	123-131	9	26
α-helix	135-137	3
β-strand	138-145	8	27
α-helix	148-150	3
α-helix	154-169	16
β-strand	175-182	8	27
α-helix	196-200	5
α-helix	204-206	3
β-strand	211	1	28
α-helix	212-213	2
β-strand	216-223	8	27
α-helix	226-234	9
β-strand	239	1	28
β-strand	246	1	29
α-helix	248-257	10
α-helix	259-262	4
β-strand	269-276	8	27
β-strand	280	1	29
α-helix	294-295	2
β-strand	301	1	30
β-strand	306	1	27
β-strand	307	1	30
α-helix	314-317	4
α-helix	318-328	11
β-strand	330-336	7	27
α-helix	338-340	3
α-helix	341-350	10
β-strand	355-358	4	27
α-helix	364-374	11
β-strand	381-382	2	31
β-strand	383-386	4	25
β-strand	392-399	8	26
α-helix	401-403	3
β-strand	405-407	3	26
β-strand	411-412	2	31
β-strand	420-429	10	26
β-strand	437-444	8	25
β-strand	451-457	7	25
α-helix	462-465	4
β-strand	482	1	32
β-strand	485	1	32
β-strand	493	1	33
β-strand	499	1	33

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

>8XFG_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

>8XFG_2 Integrin beta-3 (chains B)
MRARPRPRPLWATVLALGALAGVGVGGPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLG
SPRCDLKENLLKDNCAPESIEFPVSEARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRP
DDSKNFSIQVRQVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFG
AFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSR
NRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCH
VGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVLS
MDSSNVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDT
VSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGT
FECGVCRCGPGWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFG
KITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLL
CSGRGKCECGSCVCIQPGSYGDTCEKCPTCPDACTFKKECVECKKFDRGALHDENTCNRY
CRDEIESVKELKDTGKDAVNCTYKNEDDCVVRFQYYEDSSGKSILYVVEEPECPKGPDIL
VVLLSVMGAILLIGLAALLIWKLLITIHDRKEFAKFEEERARAKWDTANNPLYKEATSTF
TNITYRGT

Ligands and cofactors

ID	Name	Formula	Copies
A1LU7	2-[(2~{R},5~{R},8~{S},11~{S})-8-(4-azanylbutyl)-11-(3-carbamimidamidopropyl)-3,…	C27 H41 N9 O7	1

Primary citation

Cryo-EM structure of integrin ITGAV, ITGB3 and CYCLO (RGDFK) complex, conformation 1. 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

Browse structure collections

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