6DJP: Integrin alpha-v beta-8

Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68. Determined by electron microscopy at 4.8 Å resolution. Released 25 Jul 2018.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 7,307
Mol. weight: 274.9 kDa
Ligands: NAG
Released: 25 Jul 2018

Explore 6DJP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DJP contains 35 α-helices and 123 β-strands across 6 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, 53 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	23-26	4	2
β-strand	35-40	6	2
β-strand	55-60	6	2
β-strand	67-69	3	2
α-helix	70	1
α-helix	77-78	2
β-strand	79-81	3	3
β-strand	84-85	2	3
β-strand	87-88	2	4
β-strand	97-101	5	5
β-strand	104-109	6	5
β-strand	113-114	2	4
β-strand	123-124	2	4
β-strand	127-132	6	5
β-strand	135-139	5	5
β-strand	160-163	4	6
β-strand	168-172	5	6
α-helix	176-179	4
β-strand	181	1	7
β-strand	183-187	5	6
α-helix	188-193	6
β-strand	208-209	2	6
α-helix	215-217	3
β-strand	222	1	7
β-strand	225-229	5	8
β-strand	238-243	6	8
α-helix	246-249	4
β-strand	252-256	5	8
β-strand	263-268	6	8
β-strand	279-283	5	9
β-strand	292-297	6	9
β-strand	301-303	3	10
β-strand	309-311	3	10
β-strand	314-320	7	9
β-strand	326-332	7	9
α-helix	340-342	3
β-strand	343-348	6	11
β-strand	357-362	6	11
β-strand	372-376	5	11
β-strand	378-379	2	12
β-strand	382-383	2	12
β-strand	389-392	4	11
β-strand	408-412	5	1
β-strand	421-426	6	1
α-helix	427-429	3
β-strand	431-437	7	1
α-helix	438-439	2
β-strand	440-449	10	13
β-strand	453-454	2	14
β-strand	461-462	2	15
β-strand	469-470	2	15
β-strand	472-483	12	13
β-strand	490-499	10	16
β-strand	511-513	3	13
β-strand	518	1	13
β-strand	520-528	9	16
β-strand	534-542	9	13
α-helix	543-544	2
α-helix	554	1
β-strand	555-563	9	16
β-strand	577-578	2	13
β-strand	585-590	6	16
β-strand	591-592	2	14

Chain B: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	64	1	17
β-strand	76	1	18
β-strand	81-84	4	17
β-strand	91-97	7	18
β-strand	105-112	8	19
β-strand	114	1	20
α-helix	115-117	3
α-helix	118-135	18
β-strand	142-149	8	19
β-strand	182-189	8	19
α-helix	192-200	9
β-strand	205	1	20
β-strand	212	1	21
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-241	7	19
α-helix	245	1
β-strand	246	1	21
α-helix	247	1
α-helix	251-255	5
β-strand	268	1	19
β-strand	271	1	19
α-helix	279-282	4
α-helix	283-292	10
β-strand	295-302	8	19
α-helix	303-312	10
α-helix	313-315	3
β-strand	319-324	6	19
α-helix	325	1
α-helix	331-343	13
β-strand	346-347	2	22
β-strand	348-350	3	17
β-strand	357-364	8	18
β-strand	371-372	2	18
β-strand	376-377	2	22
α-helix	385	1
β-strand	386-394	9	18
β-strand	403-410	8	17
β-strand	417-422	6	17

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	23
α-helix	7-9	3
β-strand	11-12	2	24
β-strand	18-25	8	23
β-strand	35-40	6	25
β-strand	46-52	7	25
β-strand	68-72	5	23
β-strand	78-83	6	23
β-strand	92	1	26
β-strand	93-98	6	25
β-strand	113	1	26
β-strand	114-115	2	24

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	27
β-strand	10-11	2	28
β-strand	19-24	6	27
β-strand	33-36	4	28
β-strand	47	1	28
β-strand	53	1	28
α-helix	54	1
β-strand	61-66	6	27
β-strand	69-74	6	27
α-helix	77-78	2
α-helix	79-81	3
β-strand	84-89	6	28
β-strand	96-97	2	28
β-strand	101-103	3	28

Chain E: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
β-strand	10-12	3	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	34-40	7	31
β-strand	44-51	8	31
β-strand	58-60	3	31
α-helix	62-64	3
β-strand	69-73	5	29
β-strand	78-83	6	29
α-helix	88-90	3
β-strand	93-95	3	31
β-strand	97	1	32
β-strand	105	1	32
β-strand	109-110	2	31
β-strand	111-113	3	30

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	33
β-strand	10-12	3	34
β-strand	19-25	7	33
β-strand	32-38	7	34
β-strand	45-49	5	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-67	6	33
β-strand	70-75	6	33
β-strand	85-91	7	34
α-helix	96	1
β-strand	97-98	2	34
β-strand	102-105	4	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-v	A	protein	965	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	639	Homo sapiens	P26012 (AlphaFold model)
8B8 heavy chain Fab	C	protein	213	Mus musculus
8B8 light chain Fab	D	protein	213	Mus musculus
68 heavy chain Fab	E	protein	212	Mus musculus
68 light chain Fab	F	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>6DJP_1 Integrin alpha-v (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPAPM
PVPVW

Sequence of entity 2 (B), FASTA

>6DJP_2 Integrin beta-8 (chains B)
EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYP
SVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNN
IEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPH
GYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLV
MTDQTSHLALDSKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFA
VQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFN
ITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIH
IHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENKCHFDEDQFSSESCKSHKDQPVCSG
RGVCVCGKCSCHKIKLGKVYGKYCEKDDFSCPYHHGNLCAGHGECEAGRCQCFSGWEGDR
CQCPSAAAQHCVNSKGQVCSGRGTCVCGRCECTDPRSIGRFCEHCPTCYTACKENWNCMQ
CLHPHNLSQAILDQCKTSCALMEQQHYVDQTSECFSSPS

Sequence of entity 3 (C), FASTA

>6DJP_3 8B8 heavy chain Fab (chains C)
EVQLVESGPGLVKPSQSLSLTCSVTGYYITSSYYWNWIRQFPGNELEWMGYISYDGSNSY
NPSLKNRISITRDTSKNQFFLKLNSVTTEDIATYFCVREDYDSFDYWGQGTTLTVSSAKT
TAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVTSSTWPSQSITCNVAHPASSTKVDKK

Sequence of entity 4 (D), FASTA

>6DJP_4 8B8 light chain Fab (chains D)
EIVLTQSPAIMSAFPGEKVTMTCSASSSVSYIHWYQQKSGTSPKRWIYDTSKLASGVPAR
FSGSGSGTSYSLTISSMEAEDAATYYCHQWTSNPATFGGGTKLEIKAADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (E), FASTA

>6DJP_5 68 heavy chain Fab (chains E)
EVQLQQSGAELMKPGASVKISCKATGYTFSTYWIEWIKQRPGHGLEWIGDILPGSGTTNY
NEKFKGRATVTADRSSNTAYMQLSSLTSEDSAVYYCARWGWDSYWGQGTLVTVSSASTKG
PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKK

Sequence of entity 6 (F), FASTA

>6DJP_6 68 light chain Fab (chains F)
DIEMTQSPSSLSASLGDRVTISCSASQGISNYLNWYQQKPDGTVKLLIYYTSSLHSGVPS
RFSGSGSGTDYSLTISNLEPEDIATYYCQQYSELPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Cryo-EM structure of the alpha v beta 8 integrin reveals a mechanism for stabilizing integrin extension. Cormier, A., Campbell, M.G., Ito, S. et al. Nat Struct Mol Biol (2018) 25:698-704. DOI 10.1038/s41594-018-0093-x · 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
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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