5lvc

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Aichi virus 1: empty particle

Structural highlights

5lvc is a 3 chain structure with sequence from Aichivirus A. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 4.2Å
Experimental data:Check to display Experimental Data
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POLG_AIVA8 Required for viral RNA replication and viral RNA encapsidation (PubMed:14512530). Does not have any proteolytic activity (PubMed:14512530).[1] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).[2] [3] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP1 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).[4] [5] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP1 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).[6] [7] Required for viral RNA replication (PubMed:18653460). Does not have any proteolytic activity (PubMed:18653460).[8] Affects membrane integrity and causes an increase in membrane permeability. Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[UniProtKB:P03300] Serves as membrane anchor via its hydrophobic domain. Plays an essential role in viral RNA replication by recruiting PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (PubMed:22124328, PubMed:24672044, PubMed:27989622, PubMed:30755512, PubMed:22258260). Stimulates the enzymatic activity of PI4KB, this activation is sensitized by ACBD3 (PubMed:24672044, PubMed:27989622).[9] [10] [11] [12] [13] Forms a primer, VPg-pU, which is utilized by the polymerase for the initiation of RNA chains.[UniProtKB:P03304] Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate cooperatively bind to the protease (By similarity).[UniProtKB:P03304][UniProtKB:P12296] Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]

Publication Abstract from PubMed

Aichi virus 1 (AiV-1) is a human pathogen from the Kobuvirus genus of the Picornaviridae family. Worldwide, 80-95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. Unlike most picornaviruses, kobuvirus capsids are composed of only three types of subunits: VP0, VP1, and VP3. Here we present the structure of the AiV-1 virion determined to a resolution of 2.1 A using X-ray crystallography. The surface loops puff of VP0 and knob of VP3 in AiV-1 are shorter than those in other picornaviruses. Instead, the 42-residue-long BC-loop of VP0 forms the most prominent surface feature of the AiV-1 virion. We determined the structure of AiV-1 empty particle to a resolution of 4.2 A using cryo-electron microscopy. The empty capsids are expanded relative to the native virus. The N-terminal arms of capsid proteins VP0, which mediate contacts between the pentamers of capsid protein protomers in the native AiV-1 virion, are disordered in the empty capsid. Nevertheless, the empty particles are stable, at least in vitro, and do not contain pores that might serve as channels for genome release. Therefore, extensive and probably reversible local reorganization of AiV-1 capsid is required for its genome release. IMPORTANCE: Aichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80-95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from the Picornaviridae family. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid.

Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism.,Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122[14]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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References

  1. ↑ Sasaki J, Nagashima S, Taniguchi K. Aichi virus leader protein is involved in viral RNA replication and encapsidation. J Virol. 2003 Oct;77(20):10799-807. PMID:14512530 doi:10.1128/jvi.77.20.10799-10807.2003
  2. ↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
  3. ↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
  4. ↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
  5. ↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
  6. ↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
  7. ↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
  8. ↑ Sasaki J, Taniguchi K. Aichi virus 2A protein is involved in viral RNA replication. J Virol. 2008 Oct;82(19):9765-9. PMID:18653460 doi:10.1128/JVI.01051-08
  9. ↑ Sasaki J, Ishikawa K, Arita M, Taniguchi K. ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites. EMBO J. 2012 Feb 1;31(3):754-66. PMID:22124328 doi:10.1038/emboj.2011.429
  10. ↑ Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol. 2012 Apr;86(7):3605-16. PMID:22258260 doi:10.1128/JVI.06778-11
  11. ↑ Ishikawa-Sasaki K, Sasaki J, Taniguchi K. A complex comprising phosphatidylinositol 4-kinase IIIβ, ACBD3, and Aichi virus proteins enhances phosphatidylinositol 4-phosphate synthesis and is critical for formation of the viral replication complex. J Virol. 2014 Jun;88(12):6586-98. PMID:24672044 doi:10.1128/JVI.00208-14
  12. ↑ McPhail JA, Ottosen EH, Jenkins ML, Burke JE. The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIbeta, PI4KB, through ACBD3. Structure. 2016 Dec 7. pii: S0969-2126(16)30358-6. doi:, 10.1016/j.str.2016.11.016. PMID:27989622 doi:http://dx.doi.org/10.1016/j.str.2016.11.016
  13. ↑ Lyoo H, van der Schaar HM, Dorobantu CM, Rabouw HH, Strating JRPM, van Kuppeveld FJM. ACBD3 Is an Essential Pan-enterovirus Host Factor That Mediates the Interaction between Viral 3A Protein and Cellular Protein PI4KB. mBio. 2019 Feb 12;10(1):e02742-18. PMID:30755512 doi:10.1128/mBio.02742-18
  14. ↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16

Contents


5lvc, resolution 4.20Å

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