title: Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle.
abstract: During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress.
authors.affiliation: Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, A-1030 Vienna, Austria.
authors.forename: Angela
authors.initials: A
authors.lastname: Pickl-Herk
authors.forename: Daniel
authors.initials: D
authors.lastname: Luque
authors.forename: Laia
authors.initials: L
authors.lastname: Vives-Adrián
authors.forename: Jordi
authors.initials: J
authors.lastname: Querol-Audí
authors.forename: Damià
authors.initials: D
authors.lastname: Garriga
authors.forename: Benes L
authors.initials: BL
authors.lastname: Trus
authors.forename: Nuria
authors.initials: N
authors.lastname: Verdaguer
authors.forename: Dieter
authors.initials: D
authors.lastname: Blaas
authors.forename: José R
authors.initials: JR
authors.lastname: Castón
mesh_terms: D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D012229:Rhinovirus / Q000235:genetics / Q000502:physiology*; D014771:Virion / Q000737:chemistry*; D057646:Virus Uncoating / Q000502:physiology*
chemical_list: D012367:RNA, Viral
keywords: 3D cryo-EM; X-ray analysis; genome uncoating; picornavirus