5LVC: Aichi virus 1: empty particle

Name: PDB 5LVC: Aichi virus 1: empty particle
Published: 2016-12-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Aichi virus 1: empty particle. Determined by electron microscopy at 4.2 Å resolution. Released 14 Dec 2016.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Aichi virus
Chains: 3
Atoms: 5,464
Mol. weight: 90.23 kDa
Released: 14 Dec 2016

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

Secondary structure: helices and β-sheets

5LVC contains 24 α-helices and 53 β-strands across 3 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	42	1	1
α-helix	43-46	4
β-strand	51-52	2	2
α-helix	53-54	2
β-strand	55	1	3
β-strand	60	1	3
β-strand	63-66	4	2
β-strand	71-74	4	4
α-helix	77-80	4
α-helix	89-93	5
β-strand	96-110	15	2
β-strand	117-124	8	4
α-helix	128-131	4
α-helix	136-139	4
β-strand	143-149	7	4
β-strand	154-161	8	2
β-strand	170-171	2	2
β-strand	176	1	5
β-strand	177	1	6
β-strand	185	1	6
β-strand	195-201	7	4
β-strand	211-228	18	2
α-helix	230-233	4

Chain b: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	7
β-strand	33	1	7
α-helix	38	1
β-strand	39-40	2	8
β-strand	47-48	2	9
β-strand	148	1	10
β-strand	156-157	2	9
α-helix	163-164	2
β-strand	165	1	10
α-helix	168-170	3
β-strand	175-183	9	10
β-strand	191-192	2	11
β-strand	198	1	12
α-helix	207	1
α-helix	213-216	4
β-strand	224	1	12
β-strand	225-227	3	11
α-helix	229-234	6
α-helix	239-244	6
β-strand	247-259	13	10
β-strand	267-276	10	11
α-helix	280-287	8
α-helix	289-293	5
β-strand	296-300	5	11
β-strand	306-311	6	10
β-strand	320-321	2	10
β-strand	325	1	5
β-strand	328-339	12	11
α-helix	340-341	2
β-strand	347-364	18	10

Chain c: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	22-23	2	2
α-helix	28-29	2
β-strand	30-31	2	8
α-helix	32-33	2
β-strand	40-41	2	2
β-strand	43	1	1
α-helix	45-49	5
β-strand	53-57	5	13
β-strand	60	1	14
α-helix	63-64	2
β-strand	68-73	6	15
α-helix	85-92	8
β-strand	93-97	5	16
β-strand	100-106	7	13
β-strand	113-122	10	15
α-helix	131-134	4
β-strand	138-143	6	15
β-strand	149-154	6	13
β-strand	163-164	2	16
β-strand	178-189	12	15
β-strand	197	1	14
β-strand	200-206	7	13
β-strand	211-215	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	a	protein	253	Aichi virus	O91464 (AlphaFold model)
VP0	b	protein	370	Aichi virus	O91464 (AlphaFold model)
VP3	c	protein	223	Aichi virus	O91464 (AlphaFold model)

Sequence of entity 1 (a), FASTA

>5LVC_1 VP1 (chains a)
TLTEDLDAPQDTGNIENGAADNSPQPRTTFDYTGNPLPPDTKLENFFSFYRLLPMGGSGA
PSLSFPADEGTIIPLNPINWLKGADVSGIAAMLSCFTYIAADLRITLRFSNPNDNPATML
VAFAPPGATIPLKPTRQMLSNFYMAEVPVSAATSTMVSFSIPYTSPLSAIPTSYFGWEDW
SGTNFGQLSSGSWGNLMLIPSLSVDSAIPFDFQLSCWVAFGNFKAWVPRPPPPLPPLPTP
AANAERTVAVIKQ

Sequence of entity 2 (b), FASTA

>5LVC_2 VP0 (chains b)
GNSVTNIYGNGNNVTTDVGANGWAPTVSTGLGDGPVSASADSLPGRSGGASSEKTHTVSG
SSNKVGSRFSKWWEPAAARASESATDSAIEGIDAAGKAASKAITRKLDRPAAPSSTANPQ
PSLIALNPSATQSGNASILTGSTAPSLLAYPTATPVPLPNPDEPSQPGPSGDRTWLLDTV
TWSQEFTRGWNIAGSNGMQWTGLESLIFPVSTDTNWTSTSSPTAYPLPFSFVRAYPDSSW
AAMYNTHSMWNCGWRVQVTVNGSQFHAGALILYMVPEATTHAIQTARDNAGFVFPYVILN
LYESNTATIEVPYISPTPNTSSGLHAPWTFYLQVLSPLNPPPSLPTSLSCSIYVTPVDSS
FHGLRYLAPQ

Sequence of entity 3 (c), FASTA

>5LVC_3 VP3 (chains c)
HWKTRAVPGAGTFGSAVAGQELPLCGVRAYYPPNAYIPAQVRDWLEFAHRPGLMATVPWT
MADEPAERLGIFPVSPSAIAGTGAPISYVISLFSQWRGELAAHLLFTGSAQHYGRLVVCY
TPAAPQPPSTMQEAMRGTYTVWDVNAASTLEFTIPFISNSYWKTVDVNNPDALLSTTGYV
SIWVQNPLVGPHTAPASALVQAFISAGESFNVRLMQNPALTSQ

Primary citation

Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism. Sabin, C., Fuzik, T., Skubnik, K. et al. J Virol (2016) 90:10800-10810. DOI 10.1128/JVI.01601-16 · PubMed

Other PDB entries of the same protein (UniProt O91464 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZV1 1.74 Å, Crystal Structure of Aichivirus A 2A protein L64M, L109M mutant
5AOO 2.1 Å, X-ray structure of a human Kobuvirus: Aichi virus A (AiV)
7ZV6 2.83 Å, Crystal Structure of Aichivirus A 2A protein
5LZ3 3.0 Å, Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus A
5GKA 3.7 Å, cryo-EM structure of human Aichi virus

Browse structure collections

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