5NED: Foot and Mouth Disease Virus O PanAsia

Name: PDB 5NED: CryoEM Structure of Foot and Mouth Disease Virus O PanAsia
Published: 2017-06-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

CryoEM Structure of Foot and Mouth Disease Virus O PanAsia. Determined by electron microscopy at 3.1 Å resolution. Released 21 Jun 2017.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Foot-and-mouth disease virus
Chains: 4
Atoms: 5,095
Mol. weight: 80.46 kDa
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5NED contains 22 α-helices and 39 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: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	15-18	4
α-helix	32-35	4
β-strand	40-42	3	2
β-strand	48-50	3	3
α-helix	53-55	3
α-helix	61-66	6
β-strand	71-83	13	2
β-strand	86-89	4	3
α-helix	96-99	4
β-strand	105-106	2	3
α-helix	107-108	2
β-strand	113-117	5	2
β-strand	126-127	2	2
β-strand	167-169	3	3
β-strand	172-186	15	2
α-helix	193-196	4

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	15-19	5	4
β-strand	22-26	5	4
β-strand	32-34	3	5
β-strand	53-54	2	5
α-helix	56-58	3
β-strand	62-69	8	5
β-strand	78-83	6	6
α-helix	90-95	6
β-strand	98-111	14	5
β-strand	120-127	8	6
α-helix	135-142	8
β-strand	145-148	4	6
β-strand	155-160	6	5
β-strand	169	1	5
β-strand	177-185	9	6
β-strand	197-213	17	5
α-helix	214-215	2

Chain C: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	3
α-helix	22-24	3
α-helix	30-33	4
α-helix	44-50	7
β-strand	53-54	2	7
β-strand	57	1	8
β-strand	61	1	8
β-strand	63-65	3	7
α-helix	66-67	2
β-strand	73-78	6	9
α-helix	90-95	6
β-strand	98-102	5	10
β-strand	105-111	7	7
β-strand	118-126	9	9
α-helix	131-133	3
α-helix	136-139	4
β-strand	143-148	6	9
β-strand	154-159	6	7
β-strand	168-169	2	10
β-strand	183-192	10	9
β-strand	198-205	8	7
β-strand	210-214	5	10

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	23-24	2
α-helix	28-31	4
α-helix	33-35	3
α-helix	68-73	6
β-strand	76	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O PanAsia VP1	A	protein	211	Foot-and-mouth disease virus	Q98W00
O PanAsia VP2	B	protein	218	Foot-and-mouth disease virus	Q6ZZ87
O PanAsia VP3	C	protein	220	Foot-and-mouth disease virus	Q7TD07
O PanAsia VP4	D	protein	85	Foot-and-mouth disease virus	Q7TD07

Sequence of entity 1 (A), FASTA

>5NED_1 O PanAsia VP1 (chains A)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPETALDNTTNPTAYHKAPLTRLALPYT
APHRVLATAYNGNCKYGESHTTNVRGDLQVLAQKAARTLPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPSEARHKQKIVAPVKQ

Sequence of entity 2 (B), FASTA

>5NED_2 O PanAsia VP2 (chains B)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATTEDFVSGPNTSGLETRVVQAER
FFKTHLFDWVTSDSFGRCHLLELPTDHKGVYGSLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSINKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNTEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (C), FASTA

>5NED_3 O PanAsia VP3 (chains C)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLRFEGD
VPYVTTKTDSDRILAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYAYTASDTAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (D), FASTA

>5NED_4 O PanAsia VP4 (chains D)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNAISGGSNEGSTDTTSNHTT
NTQNNDWFSKLASSAFSGLFGALLA

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
5NEM 10.8 Å, Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O…
5NER 11.5 Å, Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O…

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