5NEU: O1 Manisa VP1

Name: PDB 5NEU: Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B.
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 B. Determined by electron microscopy at 12.3 Å resolution. Released 21 Jun 2017.

Method: Electron microscopy
Resolution: 12.3 Å
Organisms: Foot-and-mouth disease virus, Homo sapiens
Chains: 6
Atoms: 13,287
Mol. weight: 196.55 kDa
Ligands: MG, CA
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5NEU contains 40 α-helices and 136 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: 5 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	48-52	5	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
β-strand	164-169	6	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: 7 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
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	66-70	5	17
β-strand	79	1	18
β-strand	85	1	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	123-124	2	19
β-strand	127-132	6	20
β-strand	135-139	5	20
β-strand	162-163	2	21
β-strand	168-170	3	21
β-strand	173	1	22
α-helix	176-179	4
β-strand	182	1	22
β-strand	185-187	3	21
α-helix	188-194	7
β-strand	208	1	21
β-strand	226-227	2	23
β-strand	239-243	5	23
β-strand	252-256	5	23
β-strand	263-266	4	23
β-strand	282-283	2	24
β-strand	292-293	2	24
β-strand	294-295	2	25
β-strand	301-302	2	26
β-strand	310-311	2	26
β-strand	314-319	6	25
α-helix	326	1
β-strand	327-332	6	25
β-strand	343-348	6	27
β-strand	357-362	6	27
α-helix	367-369	3
β-strand	372-376	5	27
β-strand	378	1	28
β-strand	383	1	28
β-strand	407	1	16
β-strand	422-426	5	16
β-strand	431-435	5	16
α-helix	436	1
β-strand	437	1	15
α-helix	438	1
β-strand	440-441	2	29
β-strand	442-444	3	30
β-strand	447-450	4	31
β-strand	472-479	8	31
β-strand	480-482	3	30
β-strand	491-498	8	32
β-strand	511-513	3	31
β-strand	521-527	7	32
β-strand	529	1	30
β-strand	534-542	9	31
α-helix	543-544	2
β-strand	557-563	7	32
β-strand	577-578	2	29
β-strand	585-588	4	32

Chain B: 14 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	23-24	2	33
β-strand	25	1	34
β-strand	28-29	2	33
β-strand	37	1	34
β-strand	43-46	4	35
β-strand	67	1	36
β-strand	70-74	5	35
β-strand	80-82	3	37
β-strand	85-86	2	36
β-strand	95-102	8	38
α-helix	105-107	3
α-helix	111-114	4
α-helix	118-128	11
β-strand	132-134	3	38
β-strand	138-139	2	38
α-helix	152-155	4
α-helix	167-169	3
β-strand	172	1	38
β-strand	173	1	39
α-helix	177-178	2
β-strand	179	1	38
α-helix	183-191	9
β-strand	202	1	40
α-helix	205-210	6
β-strand	225-231	7	38
β-strand	236	1	40
α-helix	239-245	7
β-strand	262	1	39
α-helix	264-267	4
α-helix	274-283	10
β-strand	287-291	5	38
α-helix	296-306	11
β-strand	310-311	2	38
α-helix	322-332	11
β-strand	426-429	4	35
β-strand	436	1	37
β-strand	440-442	3	36
β-strand	448-450	3	36
β-strand	465-466	2	36
β-strand	469-471	3	37
β-strand	480-486	7	35
β-strand	494-497	4	35
β-strand	509	1	41
β-strand	520-523	4	41
β-strand	526-529	4	41

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	Q6PMW3
Capsid protein	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	590	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	470	Homo sapiens	P18564 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>5NEU_1 O1 Manisa VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYT
APHRVLATVYNGNSKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPDQARHKQKIVAP

Sequence of entity 2 (2), FASTA

>5NEU_2 O1 Manisa VP2 (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAER
FFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5NEU_3 Capsid protein (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGD
VPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTYTASDVAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5NEU_4 O1 Manisa VP4 (chains 4)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTT
NTQNNDWFSKLASSAFSGLFGALLA

Sequence of entity 5 (A), FASTA

>5NEU_5 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSSRMFLLVGAPKANTTQPGIVEGGQVLKCDWS
STRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQER
EPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQ
LISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSG
VPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMD
RGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAA
PYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYPDL
IVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKAD
GKGVLPRKLNFQVELLLDKLKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRD
ESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL

Sequence of entity 6 (B), FASTA

>5NEU_6 Integrin beta-6 (chains B)
GCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIENPVSQ
VEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDL
SASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIP
YFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRND
SLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQ
NNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLG
DTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLG
DALELLVSPECNCDCQKEVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
CA	Calcium ion	Ca	2

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
5NET 8.6 Å, Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease…

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