5NET: O1 Manisa VP1

Name: PDB 5NET: Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A.
Published: 2017-06-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose A. Determined by electron microscopy at 8.6 Å resolution. Released 21 Jun 2017.

Method: Electron microscopy
Resolution: 8.6 Å
Organisms: Foot-and-mouth disease virus, Homo sapiens
Chains: 6
Atoms: 13,559
Mol. weight: 201.25 kDa
Ligands: MAN, NAG, CA
Released: 21 Jun 2017

Explore 5NET in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NET contains 58 α-helices and 141 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 1: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	11	1	2
α-helix	15-18	4
β-strand	31	1	3
β-strand	40-42	3	4
β-strand	48-50	3	5
α-helix	53-55	3
α-helix	61-64	4
β-strand	69-83	15	4
β-strand	86-89	4	5
α-helix	95-98	4
β-strand	105-106	2	5
β-strand	113-116	4	4
β-strand	126-127	2	4
α-helix	140-142	3
α-helix	149-152	4
α-helix	153-156	4
β-strand	167-169	3	5
β-strand	172-188	17	4
α-helix	193-196	4
β-strand	200	1	6
β-strand	203	1	7

Chain 2: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	8
β-strand	22-25	4	8
β-strand	32-34	3	9
β-strand	52-54	3	9
α-helix	56-58	3
β-strand	62-69	8	9
β-strand	79-83	5	10
α-helix	90-95	6
β-strand	98-111	14	9
β-strand	120-127	8	10
α-helix	136-142	7
β-strand	145-148	4	10
β-strand	155-160	6	9
β-strand	169	1	9
β-strand	177-185	9	10
β-strand	197-203	7	9
β-strand	205-213	9	9
α-helix	214-216	3

Chain 3: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	20-23	4
β-strand	24	1	4
β-strand	30	1	11
α-helix	31-33	3
β-strand	40-41	2	4
β-strand	43	1	3
α-helix	44-50	7
β-strand	53-54	2	1
β-strand	57	1	12
β-strand	61	1	12
β-strand	63-65	3	1
β-strand	73-78	6	13
β-strand	83	1	6
α-helix	91-94	4
β-strand	98-102	5	14
β-strand	105-111	7	1
β-strand	118-126	9	13
α-helix	131-133	3
α-helix	138-141	4
β-strand	145-148	4	13
β-strand	154-159	6	1
β-strand	168-169	2	14
β-strand	173	1	7
β-strand	183-192	10	13
β-strand	198-205	8	1
β-strand	210-214	5	14

Chain 4: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	23-24	2
α-helix	33	1
β-strand	34	1	11
α-helix	35	1
α-helix	67-73	7
β-strand	76	1	2

Chain A: 19 helices, 58 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
α-helix	8	1
β-strand	9-12	4	16
β-strand	22-26	5	17
β-strand	35-40	6	17
β-strand	55-60	6	17
β-strand	67-70	4	17
β-strand	79-81	3	18
β-strand	84-85	2	18
β-strand	87-88	2	19
β-strand	97-101	5	20
β-strand	104-109	6	20
β-strand	113-114	2	19
β-strand	123	1	19
β-strand	127-132	6	20
β-strand	135-139	5	20
β-strand	160-163	4	21
β-strand	168-173	6	21
α-helix	176-179	4
β-strand	181	1	22
β-strand	182-187	6	21
α-helix	188-193	6
β-strand	207-209	3	21
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	22
β-strand	225-229	5	23
α-helix	237	1
β-strand	238-243	6	23
α-helix	246-249	4
β-strand	252-256	5	23
β-strand	266-268	3	23
β-strand	279-283	5	24
α-helix	291	1
β-strand	292-297	6	24
β-strand	301-303	3	25
β-strand	309-311	3	25
β-strand	314-320	7	24
α-helix	321	1
β-strand	326-332	7	24
β-strand	343-348	6	26
β-strand	357-362	6	26
α-helix	367-369	3
β-strand	372-377	6	26
β-strand	378	1	27
β-strand	383	1	27
β-strand	389-392	4	26
β-strand	404-412	9	16
β-strand	421-426	6	16
α-helix	427-429	3
β-strand	431-435	5	16
α-helix	436	1
β-strand	437	1	15
α-helix	438-439	2
β-strand	440-441	2	28
β-strand	442-443	2	29
β-strand	446-450	5	30
β-strand	453-454	2	31
β-strand	462	1	32
β-strand	469	1	32
β-strand	472-479	8	30
β-strand	481-482	2	29
β-strand	490-499	10	33
α-helix	507-509	3
β-strand	511-513	3	30
β-strand	518	1	30
β-strand	520-528	9	33
α-helix	532-533	2
β-strand	534-542	9	30
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	33
α-helix	565-568	4
β-strand	577-578	2	28
α-helix	579	1
β-strand	585-590	6	33
β-strand	591-592	2	31

Chain B: 17 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	14-19	6
β-strand	25-27	3	34
β-strand	39-40	2	34
β-strand	55-56	2	34
β-strand	61-66	6	35
α-helix	78-80	3
β-strand	84-85	2	36
β-strand	88-93	6	35
β-strand	99-106	8	36
β-strand	113-120	8	37
α-helix	128-130	3
α-helix	136-144	9
β-strand	150-157	8	37
α-helix	170-174	5
β-strand	185	1	38
α-helix	186-187	2
β-strand	190-197	8	37
α-helix	200-209	10
β-strand	213	1	38
β-strand	220	1	39
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	37
β-strand	254	1	39
α-helix	257-263	7
β-strand	275	1	40
β-strand	280	1	37
β-strand	281	1	40
α-helix	282-285	4
α-helix	288-291	4
α-helix	292-301	10
α-helix	304	1
β-strand	305-311	7	37
α-helix	315-324	10
β-strand	329-333	5	37
α-helix	340-350	11
β-strand	355-356	2	41
β-strand	357-360	4	35
β-strand	367-373	7	36
β-strand	379-381	3	36
β-strand	385-386	2	41
β-strand	391	1	42
β-strand	393	1	42
β-strand	394-402	9	36
β-strand	411-417	7	35
β-strand	424-430	7	35
α-helix	435-437	3
β-strand	441	1	43
β-strand	452-455	4	43
β-strand	458-461	4	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O1 Manisa VP1	1	protein	208	Foot-and-mouth disease virus	Q6PMW3
O1 Manisa VP2	2	protein	218	Foot-and-mouth disease virus	D1H101
O1 Manisa VP3	3	protein	220	Foot-and-mouth disease virus	Q6PMW3
O1 Manisa VP4	4	protein	85	Foot-and-mouth disease virus	D1H101
Integrin alpha-V	A	protein	594	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	470	Homo sapiens	P18564 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>5NET_1 O1 Manisa VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYT
APHRVLATVYNGNSKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPDQARHKQKIVAP

Sequence of entity 2 (2), FASTA

>5NET_2 O1 Manisa VP2 (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAER
FFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5NET_3 O1 Manisa VP3 (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLRFEGD
VPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTYTASDVAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5NET_4 O1 Manisa VP4 (chains 4)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTT
NTQNNDWFSKLASSAFSGLFGALLA

Sequence of entity 5 (A), FASTA

>5NET_5 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCD
WSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQ
EREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQ
GQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFV
SGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLF
MDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAI
AAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYP
DLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLK
ADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIA
YLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL

Sequence of entity 6 (B), FASTA

>5NET_6 Integrin beta-6 (chains B)
GCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIENPVSQ
VEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDL
SASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIP
YFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRND
SLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQ
NNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLG
DTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLG
DALELLVSPECNCDCQKEVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCE

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CA	Calcium ion	Ca	4

Primary citation

Rules of engagement between alpha v beta 6 integrin and foot-and-mouth disease virus. Kotecha, A., Wang, Q., Dong, X. et al. Nat Commun (2017) 8:15408-15408. DOI 10.1038/ncomms15408 · PubMed

Other PDB entries of the same protein (UniProt Q6PMW3), best resolution first:

5NEJ 3.1 Å, CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa
5AC9 3.2 Å, Structure-based energetics of protein interfaces guide Foot-and-Mouth disease virus…
5DDJ 3.5 Å, Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid
5NEU 12.3 Å, Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease…

Browse structure collections

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