5NEJ: Foot and Mouth Disease Virus O1 Manisa

Name: PDB 5NEJ: CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa
Published: 2017-06-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa. 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: 5,114
Mol. weight: 80.34 kDa
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5NEJ contains 18 α-helices and 40 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 1: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	15-18	4
β-strand	40-42	3	2
β-strand	48-50	3	3
α-helix	53-55	3
α-helix	61-64	4
β-strand	69-83	15	2
β-strand	86-89	4	3
α-helix	95-98	4
β-strand	105-106	2	3
β-strand	113-116	4	2
β-strand	126-127	2	2
β-strand	167-169	3	3
β-strand	172-188	17	2
α-helix	193-196	4

Chain 2: 4 helices, 14 β-strands

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

Chain 3: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	3
α-helix	20-24	5
α-helix	31-33	3
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
β-strand	73-78	6	9
α-helix	91-94	4
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	138-141	4
β-strand	145-148	4	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 4: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	23-24	2
α-helix	33-35	3
α-helix	67-73	7
β-strand	76	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O1 Manisa VP1	1	protein	211	Foot-and-mouth disease virus	Q6PMW3
O1 Manisa VP2	2	protein	218	Foot-and-mouth disease virus	Q6PMW3
O1 Manisa VP3	3	protein	220	Foot-and-mouth disease virus	Q6PMW3
O1 Manisa VP1	4	protein	85	Foot-and-mouth disease virus	D1H101

Sequence of entity 1 (1), FASTA

>5NEJ_1 O1 Manisa VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYT
APHRVLATVYNGESKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPDQARHKQKIVAPVKQ

Sequence of entity 2 (2), FASTA

>5NEJ_2 O1 Manisa VP2 (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAER
FFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5NEJ_3 O1 Manisa VP3 (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGD
VPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTYTASDVAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5NEJ_4 O1 Manisa VP1 (chains 4)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTT
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 Q6PMW3), best resolution first:

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…
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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