5AOO: Human Kobuvirus: Aichi virus A

Name: PDB 5AOO: X-ray structure of a human Kobuvirus: Aichi virus A (AiV)
Published: 2016-03-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

X-ray structure of a human Kobuvirus: Aichi virus A (AiV). Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: AICHIVIRUS A
Chains: 3
Atoms: 5,938
Mol. weight: 90.23 kDa
Released: 9 Mar 2016

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

Secondary structure: helices and β-sheets

5AOO contains 30 α-helices and 54 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12-13	2	1
α-helix	15-17	3
α-helix	24-26	3
α-helix	36-38	3
β-strand	42	1	2
α-helix	43-46	4
β-strand	51-53	3	3
α-helix	54	1
β-strand	55	1	4
β-strand	60	1	4
β-strand	63-66	4	3
β-strand	71-74	4	5
α-helix	77-80	4
α-helix	89-93	5
β-strand	96-110	15	3
β-strand	117-124	8	5
α-helix	128-131	4
α-helix	136-139	4
β-strand	143-149	7	5
β-strand	154-161	8	3
β-strand	170-171	2	3
β-strand	176	1	6
β-strand	177	1	7
β-strand	185	1	7
β-strand	195-201	7	5
β-strand	211-228	18	3
α-helix	230-232	3

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	8
β-strand	33	1	8
α-helix	38	1
β-strand	39-40	2	9
α-helix	41	1
β-strand	47-48	2	10
α-helix	119-121	3
β-strand	129-133	5	11
β-strand	136-140	5	11
β-strand	146-148	3	12
β-strand	156-157	2	10
α-helix	163-164	2
β-strand	165	1	12
α-helix	168-170	3
β-strand	175-183	9	12
β-strand	191-192	2	13
β-strand	198	1	14
α-helix	206-207	2
α-helix	213-216	4
β-strand	224	1	14
β-strand	225-227	3	13
α-helix	229-234	6
α-helix	239-244	6
β-strand	247-259	13	12
β-strand	267-276	10	13
α-helix	280-287	8
α-helix	289-293	5
β-strand	296-300	5	13
β-strand	306-311	6	12
β-strand	320-321	2	12
β-strand	325	1	6
β-strand	328-339	12	13
α-helix	340-341	2
β-strand	347-364	18	12

Chain C: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	22-23	2	3
α-helix	28-29	2
β-strand	30-31	2	9
α-helix	32-33	2
β-strand	40-41	2	3
β-strand	43	1	2
α-helix	45-49	5
β-strand	53-60	8	1
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	1
β-strand	113-122	10	15
α-helix	131-134	4
β-strand	138-143	6	15
β-strand	149-154	6	1
β-strand	163-164	2	16
β-strand	178-189	12	15
β-strand	197-206	10	1
β-strand	211-215	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP0	A	protein	253	AICHIVIRUS A	O91464 (AlphaFold model)
VP1	B	protein	370	AICHIVIRUS A	O91464 (AlphaFold model)
VP3	C	protein	223	AICHIVIRUS A	O91464 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5AOO_1 VP0 (chains A)
TLTEDLDAPQDTGNIENGAADNSPQPRTTFDYTGNPLPPDTKLENFFSFYRLLPMGGSGA
PSLSFPADEGTIIPLNPINWLKGADVSGIAAMLSCFTYIAADLRITLRFSNPNDNPATML
VAFAPPGATIPLKPTRQMLSNFYMAEVPVSAATSTMVSFSIPYTSPLSAIPTSYFGWEDW
SGTNFGQLSSGSWGNLMLIPSLSVDSAIPFDFQLSCWVAFGNFKAWVPRPPPPLPPLPTP
AANAERTVAVIKQ

Sequence of entity 2 (B), FASTA

>5AOO_2 VP1 (chains B)
GNSVTNIYGNGNNVTTDVGANGWAPTVSTGLGDGPVSASADSLPGRSGGASSEKTHTVSG
SSNKVGSRFSKWWEPAAARASESATDSAIEGIDAAGKAASKAITRKLDRPAAPSSTANPQ
PSLIALNPSATQSGNASILTGSTAPSLLAYPTATPVPLPNPDEPSQPGPSGDRTWLLDTV
TWSQEFTRGWNIAGSNGMQWTGLESLIFPVSTDTNWTSTSSPTAYPLPFSFVRAYPDSSW
AAMYNTHSMWNCGWRVQVTVNGSQFHAGALILYMVPEATTHAIQTARDNAGFVFPYVILN
LYESNTATIEVPYISPTPNTSSGLHAPWTFYLQVLSPLNPPPSLPTSLSCSIYVTPVDSS
FHGLRYLAPQ

Sequence of entity 3 (C), FASTA

>5AOO_3 VP3 (chains C)
HWKTRAVPGAGTFGSAVAGQELPLCGVRAYYPPNAYIPAQVRDWLEFAHRPGLMATVPWT
MADEPAERLGIFPVSPSAIAGTGAPISYVISLFSQWRGELAAHLLFTGSAQHYGRLVVCY
TPAAPQPPSTMQEAMRGTYTVWDVNAASTLEFTIPFISNSYWKTVDVNNPDALLSTTGYV
SIWVQNPLVGPHTAPASALVQAFISAGESFNVRLMQNPALTSQ

Primary citation

The Use of Noncrystallographic Symmetry Averaging to Solve Structures from Data Affected by Perfect Hemihedral Twinning. Sabin, C., Plevka, P. Acta Crystallogr Sect F Struct Biol Cryst Commun (2016) 72:188. DOI 10.1107/S2053230X16000923 · 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
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
5LVC 4.2 Å, Aichi virus 1: empty particle

Browse structure collections

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