5NEM: Localised reconstruction of alpha v beta 6

Name: PDB 5NEM: Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A.
Published: 2017-06-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A. Determined by electron microscopy at 10.8 Å resolution. Released 21 Jun 2017.

Method: Electron microscopy
Resolution: 10.8 Å
Organisms: Foot-and-mouth disease virus - type O, Homo sapiens
Chains: 6
Atoms: 13,637
Mol. weight: 199.47 kDa
Ligands: CA, NAG, MAN
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5NEM contains 59 α-helices and 138 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	11	1	2
α-helix	15-18	4
α-helix	22-24	3
β-strand	31	1	3
α-helix	32-35	4
β-strand	39-42	4	4
β-strand	48-50	3	5
α-helix	53-55	3
α-helix	61-66	6
β-strand	69-83	15	4
β-strand	86-89	4	5
α-helix	96-99	4
β-strand	105-106	2	5
β-strand	113-117	5	4
β-strand	126-127	2	4
α-helix	149-152	4
β-strand	167-169	3	5
β-strand	172-188	17	4
α-helix	194-196	3
β-strand	200	1	6

Chain 2: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	7
β-strand	15-19	5	8
β-strand	22-26	5	8
β-strand	28	1	7
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	80-83	4	10
α-helix	92-94	3
β-strand	98-111	14	9
β-strand	117-127	11	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	177-189	13	10
β-strand	197-213	17	9
α-helix	214-215	2

Chain 3: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	4
β-strand	30	1	11
α-helix	31-33	3
β-strand	40	1	4
β-strand	43	1	3
α-helix	44-50	7
β-strand	53-54	2	1
β-strand	63-64	2	1
β-strand	73-78	6	12
β-strand	83	1	6
α-helix	85-88	4
α-helix	90-94	5
α-helix	95-97	3
β-strand	98-102	5	13
β-strand	105-111	7	1
β-strand	118-126	9	12
α-helix	131-133	3
α-helix	136-139	4
β-strand	143-148	6	12
β-strand	154-159	6	1
β-strand	168-169	2	13
β-strand	183-192	10	12
β-strand	199-205	7	1
β-strand	210-214	5	13

Chain 4: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-31	4
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	14
α-helix	8	1
β-strand	9-12	4	15
β-strand	22-26	5	16
β-strand	35-40	6	16
β-strand	55-60	6	16
β-strand	67-70	4	16
β-strand	79-81	3	17
β-strand	84-85	2	17
β-strand	87-88	2	18
β-strand	97-101	5	19
β-strand	104-109	6	19
β-strand	113-114	2	18
β-strand	123	1	18
β-strand	127-132	6	19
β-strand	135-139	5	19
β-strand	160-163	4	20
β-strand	168-173	6	20
α-helix	176-179	4
β-strand	181	1	21
β-strand	182-187	6	20
α-helix	188-193	6
β-strand	207-209	3	20
α-helix	210-212	3
α-helix	215-217	3
β-strand	222	1	21
β-strand	225-229	5	22
α-helix	237	1
β-strand	238-243	6	22
α-helix	246-249	4
β-strand	252-256	5	22
β-strand	266-268	3	22
β-strand	279-283	5	23
α-helix	291	1
β-strand	292-297	6	23
β-strand	301-303	3	24
β-strand	309-311	3	24
β-strand	314-320	7	23
α-helix	321	1
β-strand	326-332	7	23
β-strand	343-348	6	25
β-strand	357-362	6	25
α-helix	367-369	3
β-strand	372-377	6	25
β-strand	378	1	26
β-strand	383	1	26
β-strand	389-392	4	25
β-strand	404-412	9	15
β-strand	421-426	6	15
α-helix	427-429	3
β-strand	431-435	5	15
α-helix	436	1
β-strand	437	1	14
α-helix	438-439	2
β-strand	440-441	2	27
β-strand	442-443	2	28
β-strand	446-450	5	29
β-strand	453-454	2	30
β-strand	462	1	31
β-strand	469	1	31
β-strand	472-479	8	29
β-strand	481-482	2	28
β-strand	490-499	10	32
α-helix	507-509	3
β-strand	511-513	3	29
β-strand	518	1	29
β-strand	520-528	9	32
α-helix	532-533	2
β-strand	534-542	9	29
α-helix	543-544	2
α-helix	545-547	3
β-strand	555-563	9	32
α-helix	565-568	4
β-strand	577-578	2	27
α-helix	579	1
β-strand	585-590	6	32
β-strand	591-592	2	30

Chain B: 17 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	14-19	6
β-strand	25-27	3	33
β-strand	39-40	2	33
β-strand	55-56	2	33
β-strand	61-66	6	34
α-helix	78-80	3
β-strand	84-85	2	35
β-strand	88-93	6	34
β-strand	99-106	8	35
β-strand	113-120	8	36
α-helix	128-130	3
α-helix	136-144	9
β-strand	150-157	8	36
α-helix	170-174	5
β-strand	185	1	37
α-helix	186-187	2
β-strand	190-197	8	36
α-helix	200-209	10
β-strand	213	1	37
β-strand	220	1	38
α-helix	222-231	10
α-helix	233-236	4
β-strand	243-250	8	36
β-strand	254	1	38
α-helix	257-263	7
β-strand	275	1	39
β-strand	280	1	36
β-strand	281	1	39
α-helix	282-285	4
α-helix	288-291	4
α-helix	292-301	10
α-helix	304	1
β-strand	305-311	7	36
α-helix	315-324	10
β-strand	329-333	5	36
α-helix	340-350	11
β-strand	355-356	2	40
β-strand	357-360	4	34
β-strand	367-373	7	35
β-strand	379-381	3	35
β-strand	385-386	2	40
β-strand	391	1	41
β-strand	393	1	41
β-strand	394-402	9	35
β-strand	411-417	7	34
β-strand	424-430	7	34
α-helix	435-437	3
β-strand	441	1	42
β-strand	452-455	4	42
β-strand	458-461	4	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O PanAsia VP1	1	protein	210	Foot-and-mouth disease virus - type O	Q98W00
O PanAsia VP2	2	protein	214	Foot-and-mouth disease virus - type O	Q6ZZ87
O PanAsia VP3	3	protein	220	Foot-and-mouth disease virus - type O	Q6ZZ87
O PanAsia VP4	4	protein	70	Foot-and-mouth disease virus - type O	A6Y878
Integrin alpha-V	A	protein	590	Homo sapiens	P06756 (AlphaFold model)
Integrin beta-6	B	protein	470	Homo sapiens	P18564

Sequence of entity 1 (1), FASTA

>5NEM_1 O PanAsia VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPETALDNTTNPTAYHKAPLTRLALPYT
APHRVLATAYNGNCKYGESHTTNVRGDLQVLAQKVARTLPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPSEARHKQKIVAPVK

Sequence of entity 2 (2), FASTA

>5NEM_2 O PanAsia VP2 (chains 2)
EETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATTEDFVSGPNTSGLETRVVQAERFFKT
HLFDWVTSDSFGRCHLLELPTDHKGVYGSLTDSYAYMRNGWDVEVTAVGNQFNGGCLLVA
MVPELCSINKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLVVMVV
APLTVNTEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5NEM_3 O PanAsia VP3 (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLRFEGD
VPYVTTKTDSDRILAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYAYTASDTAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5NEM_4 O PanAsia VP4 (chains 4)
SGNTGSIINNYYMQQYQNSMDTQLGDNAISGGSNEGSLTYFPHTTNTQNNDWFSKLASSA
FSGLFGALLA

Sequence of entity 5 (A), FASTA

>5NEM_5 Integrin alpha-V (chains A)
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSSRMFLLVGAPKANTTQPGIVEGGQVLKCDWS
STRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQER
EPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQ
LISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSG
VPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMD
RGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAA
PYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSCPPSFGYSMKGATDIDKNGYPDL
IVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKAD
GKGVLPRKLNFQVELLLDKLKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRD
ESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILL

Sequence of entity 6 (B), FASTA

>5NEM_6 Integrin beta-6 (chains B)
GCALGGAETCEDCLLIGPQCAWCAQENFTHPSGVGERCDTPANLLAKGCQLNFIENPVSQ
VEILKNKPLSVGRQKNSSDIVQIAPQSLILKLRPGGAQTLQVHVRQTEDYPVDLYYLMDL
SASMDDDLNTIKELGSRLSKEMSKLTSNFRLGFGSFVEKPVSPFVKTTPEEIANPCSSIP
YFCLPTFGFKHILPLTNDAERFNEIVKNQKISANIDTPEGGFDAIMQAAVCKEKIGWRND
SLHLLVFVSDADSHFGMDSKLAGIVCPNDGLCHLDSKNEYSMSTVLEYPTIGQLIDKLVQ
NNVLLIFAVTQEQVHLYENYAKLIPGATVGLLQKDSGNILQLIISAYEELRSEVELEVLG
DTEGLNLSFTAICNNGTLFQHQKKCSHMKVGDTASFSVTVNIPHCERRSRHIIIKPVGLG
DALELLVSPECNCDCQKEVEVNSSKCHNGNGSFQCGVCACHPGHMGPRCE

Ligands and cofactors

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

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 Q98W00), best resolution first:

5NE4 2.3 Å, Crystal Structure of Foot and Mouth Disease Virus O PanAsia
5NED 3.1 Å, CryoEM Structure of Foot and Mouth Disease Virus O PanAsia
5NER 11.5 Å, Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O…

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