Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

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.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 110, Issue 50, Page 20063-20068, Year 2013
Publish date	Dec 10, 2013
Authors	Angela Pickl-Herk / Daniel Luque / Laia Vives-Adrián / Jordi Querol-Audí / Damià Garriga / Benes L Trus / Nuria Verdaguer / Dieter Blaas / José R Castón /
PubMed 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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:24277846 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	6.5 - 10.9 Å
Structure data	EMDB-2106: HRV2 empty native capsid Method: EM (single particle) / Resolution: 10.9 Å EMDB-2107: HRV2 full native capsid Method: EM (single particle) / Resolution: 8.2 Å EMDB-2108: HRV2 empty 135S particle Method: EM (single particle) / Resolution: 9.9 Å EMDB-2109: HRV2 full 135S particle Method: EM (single particle) / Resolution: 8.8 Å PDB-4l3b: X-ray structure of the HRV2 A particle uncoating intermediate Method: X-RAY DIFFRACTION / Resolution: 6.5 Å
Source	human rhinovirus a2
Keywords	VIRUS / HRV2 capsid