5AC9: VP1

Name: PDB 5AC9: Structure-based energetics of protein interfaces guide Foot-and-Mouth disease virus vaccine design
Published: 2015-09-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure-based energetics of protein interfaces guide Foot-and-Mouth disease virus vaccine design. Determined by electron microscopy at 3.2 Å resolution. Released 23 Sept 2015.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: FOOT-AND-MOUTH DISEASE VIRUS - TYPE O
Chains: 4
Atoms: 5,115
Mol. weight: 79.98 kDa
Released: 23 Sept 2015

Explore 5AC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AC9 contains 24 α-helices and 48 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	17	1	2
β-strand	19	1	2
α-helix	28-30	3
α-helix	32-35	4
β-strand	40-42	3	3
β-strand	49-50	2	4
α-helix	61-66	6
β-strand	69-75	7	5
β-strand	76-83	8	3
β-strand	86-89	4	4
α-helix	95-99	5
β-strand	105-106	2	4
β-strand	113-117	5	3
β-strand	126-127	2	5
β-strand	167-169	3	4
β-strand	172-178	7	3
β-strand	181-188	8	5

Chain 2: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	6
β-strand	17	1	7
β-strand	24	1	7
β-strand	28	1	6
α-helix	32	1
β-strand	33-34	2	8
α-helix	35	1
α-helix	46-48	3
β-strand	53-54	2	8
α-helix	56-58	3
β-strand	62-70	9	8
β-strand	79-83	5	9
α-helix	90-95	6
β-strand	98-110	13	8
β-strand	118	1	10
β-strand	121-127	7	9
α-helix	135-142	8
β-strand	145-148	4	9
β-strand	155-160	6	8
β-strand	169	1	8
β-strand	177-183	7	9
β-strand	188	1	10
β-strand	196-213	18	8
α-helix	214-216	3

Chain 3: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	4
α-helix	20-24	5
α-helix	31-33	3
α-helix	44-50	7
β-strand	53-54	2	11
β-strand	57	1	12
β-strand	61	1	12
β-strand	63-65	3	11
β-strand	73-78	6	13
α-helix	90-95	6
β-strand	98-102	5	14
α-helix	104	1
β-strand	105-111	7	11
β-strand	118-126	9	13
α-helix	127	1
α-helix	131-133	3
α-helix	136-139	4
β-strand	145-148	4	13
β-strand	154-156	3	11
α-helix	158	1
β-strand	159	1	11
α-helix	160-161	2
β-strand	168-169	2	14
β-strand	183-192	10	13
β-strand	198-205	8	11
β-strand	210-214	5	14

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
VP1	1	protein	208	FOOT-AND-MOUTH DISEASE VIRUS - TYPE O	Q6PMW3
VP3	2	protein	218	FOOT-AND-MOUTH DISEASE VIRUS - TYPE O	Q6PMW3
VP2	3	protein	220	FOOT-AND-MOUTH DISEASE VIRUS - TYPE O	Q6PMW3
VP4	4	protein	85	FOOT-AND-MOUTH DISEASE VIRUS - TYPE O	Q6PMW3

Sequence of entity 1 (1), FASTA

>5AC9_1 VP1 (chains 1)
TTSAGESADPVTATVENYGGETQVQRRQHTDVSFILDRFVKVTPKDQINVLDLMQTPAHT
LVGALLRTATYYFADLEVAVKHEGNLTWVPNGAPEAALDNTTNPTAYHKAPLTRLALPYT
APHRVLATVYNGESKYGDGTVANVRGDLQVLAQKAARALPTSFNYGAIKATRVTELLYRM
KRAETYCPRPLLAIHPDQARHKQKIVAP

Sequence of entity 2 (2), FASTA

>5AC9_2 VP3 (chains 2)
DKKTEETTLLEDRILTTRNGHTTSTTQSSVGVTYGYATAEDFVSGPNTSGLETRVAQAER
FFKTHLFDWVTSDPFGRCHLLELPTDHKGVYGYLTDSYAYMRNGWDVEVTAVGNQFNGGC
LLVAMVPELCSIQKRELYQLTLFPHQFINPRTNMTAHITVPFVGVNRYDQYKVHKPWTLV
VMVVAPLTVNSEGAPQIKVYANIAPTNVHVAGEFPSKE

Sequence of entity 3 (3), FASTA

>5AC9_3 VP2 (chains 3)
GIFPVACSDGYGGLVTTDPKTADPAYGKVFNPPRNMLPGRFTNFLDVAEACPTFLHFEGD
VPYVTTKTDSDRVLAQFDLSLAAKHMSNTFLAGLAQYYTQYSGTINLHFMFTGPTDAKAR
YMIAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTYTASDVAETTNV
QGWVCLFQITHGKADGDALVVLASAGKDFELRLPVDARTQ

Sequence of entity 4 (4), FASTA

>5AC9_4 VP4 (chains 4)
GAGQSSPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDNATSGGSNEGSTDTTSTHTT
NTQNNDWFSKLASSAFSGLFGALLA

Primary citation

Structure-Based Energetics of Protein Interfaces Guide Foot-and-Mouth Disease Vaccine Design. Kotecha, A., Seago, J., Scott, K. et al. Nat Struct Mol Biol (2015) 22:788. DOI 10.1038/NSMB.3096 · 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
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…

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