6UJC: Integrin alpha-v beta-8

Integrin alpha-v beta-8 in complex with the Fabs C6-RGD3 and 11D12v2. Determined by electron microscopy at 3.56 Å resolution. Released 5 Feb 2020.

Method: Electron microscopy
Resolution: 3.56 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 9,209
Mol. weight: 244.92 kDa
Ligands: MG, NAG, CA
Released: 5 Feb 2020

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

Secondary structure: helices and β-sheets

6UJC contains 41 α-helices and 98 β-strands across 4 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, 51 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	55-59	5	2
β-strand	67-69	3	2
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	1	4
β-strand	127-132	6	5
β-strand	135-139	5	5
β-strand	160-164	5	6
β-strand	168-173	6	6
α-helix	176-179	4
β-strand	181	1	7
β-strand	182-187	6	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	280-283	4	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
β-strand	343-348	6	11
β-strand	357-362	6	11
α-helix	367-369	3
β-strand	372-376	5	11
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	440-441	2	12
β-strand	442-450	9	13
β-strand	453-454	2	14
β-strand	461-462	2	15
β-strand	469-470	2	15
β-strand	472-482	11	13
β-strand	490-499	10	14
α-helix	508-509	2
β-strand	511-513	3	13
β-strand	518	1	13
β-strand	520-528	9	14
α-helix	532-533	2
β-strand	534-542	9	13
β-strand	554-563	10	14
α-helix	574-576	3
β-strand	577-578	2	12
β-strand	585-592	8	14

Chain B: 24 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	16
α-helix	70-71	2
β-strand	76-77	2	17
β-strand	80-85	6	16
β-strand	90-97	8	17
α-helix	99-100	2
β-strand	103-112	10	18
α-helix	115-117	3
α-helix	118-121	4
α-helix	122-126	5
α-helix	128-134	7
α-helix	135-137	3
β-strand	139-149	11	18
α-helix	162-167	6
α-helix	176-179	4
β-strand	182-189	8	18
α-helix	192-200	9
α-helix	202-204	3
β-strand	212	1	19
α-helix	214-223	10
α-helix	225-228	4
β-strand	235-242	8	18
α-helix	245	1
β-strand	246	1	19
α-helix	247-248	2
α-helix	249-255	7
α-helix	259-261	3
β-strand	267	1	20
β-strand	271	1	18
β-strand	272	1	20
α-helix	280-282	3
α-helix	283-292	10
β-strand	295-301	7	18
α-helix	306-310	5
α-helix	313-315	3
β-strand	320-323	4	18
α-helix	324-325	2
α-helix	331-342	12
β-strand	346	1	21
β-strand	348-352	5	16
β-strand	357-364	8	17
β-strand	370-372	3	17
α-helix	373-375	3
β-strand	377	1	21
β-strand	386-394	9	17
β-strand	405-410	6	16
β-strand	417-423	7	16

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	22
β-strand	10-12	3	23
β-strand	18-25	8	22
α-helix	29-31	3
β-strand	33-39	7	23
β-strand	45-52	8	23
β-strand	57-60	4	23
β-strand	68-73	6	22
α-helix	74-76	3
β-strand	78-83	6	22
α-helix	88-90	3
β-strand	92-98	7	23
β-strand	105-106	2	23
β-strand	110-114	5	23

Chain F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	30	1	26
α-helix	39-40	2
β-strand	41	1	26
β-strand	43-48	6	25
β-strand	55-59	5	25
β-strand	63-64	2	25
α-helix	65	1
β-strand	72-77	6	24
β-strand	80-85	6	24
α-helix	90-92	3
β-strand	95-100	6	25
β-strand	106-107	2	25
β-strand	111-115	5	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-V	A	protein	1018	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-8	B	protein	727	Homo sapiens	P26012 (AlphaFold model)
C6-RGD3 heavy chain Fab	E	protein	212	Mus musculus
C6-RGD3 light chain Fab	F	protein	223	Mus musculus

Sequence of entity 1 (A), FASTA

>6UJC_1 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDN
VCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNN
EALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSS
NLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIY
ELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQT
TEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVK
SLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQPAPM
PVPVWVIILAVLAGLLLLAVLVFVMYRMGFFKRVRPPQEEQEREQLQPHENGEGNSET

Sequence of entity 2 (B), FASTA

>6UJC_2 Integrin beta-8 (chains B)
EDNRCASSNAASCARCLALGPECGWCVQEDFISGGSRSERCDIVSNLISKGCSVDSIEYP
SVHVIIPTENEINTQVTPGEVSIQLRPGAEANFMLKVHPLKKYPVDLYYLVDVSASMHNN
IEKLNSVGNDLSRKMAFFSRDFRLGFGSYVDKTVSPYISIHPERIHNQCSDYNLDCMPPH
GYIHVLSLTENITEFEKAVHRQKISGNIDTPEGGFDAMLQAAVCESHIGWRKEAKRLLLV
MTDQTSHLALDSKLAGIVVPNDGNCHLKNNVYVKSTTMEHPSLGQLSEKLIDNNINVIFA
VQGKQFHWYKDLLPLLPGTIAGEIESKAANLNNLVVEAYQKLISEVKVQVENQVQGIYFN
ITAICPDGSRKPGMEGCRNVTSNDEVLFNVTVTMKKCDVTGGKNYAIIKPIGFNETAKIH
IHRNCSCQCEDNRGPKGKCVDETFLDSKCFQCDENKCHFDEDQFSSESCKSHKDQPVCSG
RGVCVCGKCSCHKIKLGKVYGKYCEKDDFSCPYHHGNLCAGHGECEAGRCQCFSGWEGDR
CQCPSAAAQHCVNSKGQVCSGRGTCVCGRCECTDPRSIGRFCEHCPTCYTACKENWNCMQ
CLHPHNLSQAILDQCKTSCALMEQQHYVDQTSECFSSPSYLRIFFIIFIVTFLIGLLKVL
IIRQVILQWNSNKIKSSSDYRVSASKKDKLILQSVCTRAVTYRREKPEEIKMDISKLNAH
ETFRCNF

Sequence of entity 3 (E), FASTA

>6UJC_3 C6-RGD3 heavy chain Fab (chains E)
QIQLVQSGPELKKPGETVKISCKASGYTFTDYSMHWVKQAPGKGLKWVARINTETGEPTF
ADDFRGRFAVSLETSASTAYLQINNLKNEDTATYFCAIFYYGRDSWGQGTTLTVSSAKTT
APSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQSITCNVAHPASSTKVDKK

Sequence of entity 4 (F), FASTA

>6UJC_4 C6-RGD3 light chain Fab (chains F)
DIVMTQSPSSLAVSAGEKVTMSCKSSQSLLGRGDLGRLKKNALAWYQQKPGQSPRLLIYW
ASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLLSFGAGTKLELKAADA
APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDS
TYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CA	Calcium ion	Ca	5

Primary citation

Cryo-EM Reveals Integrin-Mediated TGF-beta Activation without Release from Latent TGF-beta. Campbell, M.G., Cormier, A., Ito, S. et al. Cell (2020) 180:490. DOI 10.1016/j.cell.2019.12.030 · 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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