5GKA: Human Aichi virus

Name: PDB 5GKA: cryo-EM structure of human Aichi virus
Published: 2016-09-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

cryo-EM structure of human Aichi virus. Determined by electron microscopy at 3.7 Å resolution. Released 21 Sept 2016.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Aichi virus (strain Human/A846/88/1989)
Chains: 3
Atoms: 6,087
Mol. weight: 90.13 kDa
Released: 21 Sept 2016

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

Secondary structure: helices and β-sheets

5GKA contains 29 α-helices and 50 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: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	23-25	3
α-helix	36-38	3
α-helix	43-46	4
β-strand	51-52	2	1
α-helix	53-55	3
β-strand	63-66	4	1
β-strand	71	1	2
β-strand	74	1	3
α-helix	77-81	5
α-helix	89-92	4
α-helix	93-95	3
β-strand	96	1	4
β-strand	98-100	3	5
β-strand	104-110	7	1
β-strand	117-123	7	2
α-helix	125	1
α-helix	129-131	3
α-helix	136-140	5
β-strand	145-149	5	2
β-strand	155	1	1
β-strand	158	1	1
β-strand	170-171	2	5
β-strand	195	1	3
β-strand	196-201	6	2
β-strand	211-219	9	1
β-strand	224-225	2	5
β-strand	228	1	4
α-helix	230-233	4
α-helix	235-239	5

Chain B: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	71-72	2
α-helix	120-122	3
β-strand	130-132	3	6
β-strand	139-141	3	6
β-strand	144	1	7
β-strand	147	1	8
α-helix	152-156	5
β-strand	176-177	2	8
α-helix	179-181	3
β-strand	182-183	2	9
β-strand	199	1	10
α-helix	200	1
α-helix	202-204	3
β-strand	225	1	10
β-strand	226-227	2	11
α-helix	228-233	6
α-helix	240-243	4
β-strand	251-260	10	8
β-strand	272-273	2	12
β-strand	276-277	2	11
α-helix	281-284	4
α-helix	292-294	3
β-strand	305	1	7
β-strand	307-312	6	8
β-strand	321	1	8
α-helix	322	1
β-strand	329-331	3	11
β-strand	333-334	2	12
α-helix	341-342	2
β-strand	349-350	2	9
β-strand	352-362	11	8

Chain C: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	2
α-helix	46-49	4
β-strand	53-61	9	13
β-strand	69-71	3	14
β-strand	74	1	14
α-helix	77-81	5
α-helix	88-93	6
β-strand	94-98	5	15
β-strand	101-106	6	13
β-strand	108	1	13
β-strand	114-122	9	14
α-helix	132-135	4
β-strand	140-144	5	14
β-strand	150-152	3	13
β-strand	164-165	2	15
β-strand	180-190	11	14
β-strand	198-207	10	13
β-strand	212-216	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
capsid protein VP1	A	protein	253	Aichi virus (strain Human/A846/88/1989)	O91464 (AlphaFold model)
capsid protein VP0	B	protein	367	Aichi virus (strain Human/A846/88/1989)	O91464 (AlphaFold model)
Genome polyprotein	C	protein	222	Aichi virus (strain Human/A846/88/1989)	O91464 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GKA_1 capsid protein VP1 (chains A)
TLTEDLDAPQDTGNIENGAADNSPQPRTTFDYTGNPLPPDTKLENFFSFYRLLPMGGSGA
PSLSFPADEGTIIPLDPINWLKGADVSGIAAMLSCFTYIAADLRITLRFSNPNDNPATML
VAFAPPGATIPLKPTRQMLSNFYMAEVPVSAATSTMVSFSIPYTSPLSAIPTSYFGWEDW
SGTNFGQLSSGSWGNLMLIPSLSVDSAIPFDFQLSCWVAFGNFKAWVPRPPPPLPPLPTP
AANAERTVAVIKQ

Sequence of entity 2 (B), FASTA

>5GKA_2 capsid protein VP0 (chains B)
TNIYGNGNNVNTDVGANGWAPTVSTGLGDGPVSCTPPTPSPGDTEVPPPRKPFTFPAPPT
KSGSRFSKWWEPAAARASESATDSAIEGIDAAGKAASKAITRKLDRPAAPSSTANPQPSL
IALNPSATQSGNASILTGSTAPSLLAYPTATPVPLPNPDEPSQPGPSGDRTWLLDTVTWS
QEFTRGWNIAGSNGMQWTGLESLIFPVSTDTNWTSTSSPTAYPLPFSFVRAYPDSSWAAM
YNTHSMWNCGWRVQVTVNGSQFHAGALILYMVPEATTHAIQTARDNAGFVFPYVILNLYE
SNTATIEVPYISPTPNTSSGLHAPWTFYLQVLSPLNPPPSLPTSLSCSIYVTPVDSSFHG
LRYLAPQ

Sequence of entity 3 (C), FASTA

>5GKA_3 Genome polyprotein (chains C)
HWKTRAVPGAGTFGSAVAGQELPLCGVRAYYPPNAYIPAQVRDWLEFAHRPGLMATVPWT
MADEPAERLGIFPVSPSAIAGTGAPISYVISLFSQWRGELAAHLLFTGSAQHYGRLVVCY
TPAAPQPPSTMQEAMRGTYTVWDVNAASTLEFTIPFISNSYWKTVDVNNPDALLSTTGYV
SIWVQNPLVGPHTAPASALVQAFISAGESFNVRLMQNPALTS

Primary citation

Structure of human Aichi virus and implications for receptor binding. Zhu, L., Wang, X., Ren, J. et al. Nat Microbiol (2016) 1:16150-16150. DOI 10.1038/nmicrobiol.2016.150 · 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
5LVC 4.2 Å, Aichi virus 1: empty particle

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