9G0B
Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius)
Summary for 9G0B
| Entry DOI | 10.2210/pdb9g0b/pdb |
| EMDB information | 50930 |
| Descriptor | Capsid protein VP1, Capsid protein VP2, Capsid protein VP3, ... (5 entities in total) |
| Functional Keywords | uncoating intermediate, pocket factor, lauric acid, virus |
| Biological source | rhinovirus A2 More |
| Total number of polymer chains | 4 |
| Total formula weight | 94948.77 |
| Authors | Real-Hohn, A.,Blaas, D. (deposition date: 2024-07-07, release date: 2024-07-31, Last modification date: 2025-10-29) |
| Primary citation | Real-Hohn, A.,Blaas, D. New rhinovirus uncoating intermediate reveals how sodium versus potassium ions influence RNA release. Sci Rep, 15:36768-36768, 2025 Cited by PubMed Abstract: Electron microscopy (EM) of rhinovirus A2 (RV-A2) incubated in Na phosphate buffer (pH 7.6) for 12 h at 25 °C revealed partial fragmentation, whereas upon incubation in K phosphate buffer, RV-A2 appeared intact. In buffers adjusted to pH 5.8, these differences became more pronounced; acidic Na phosphate buffer promoted disintegration of the particles, whereas in acidic K phosphate buffer, the virus appeared like native. Incubation in the acidic buffers for one hour at 4 °C followed by neutralisation resulted in the respective formation of non-infectious A particles (in Na) and a non-infectious novel uncoating intermediate (in K), which we termed 'E0 particle'. Negative staining EM revealed phosphotungstate penetration into A particles, but not into E0 particles. Cryo-EM image reconstruction of the E0 particle showed clear differences between A and E0 particles; like native virus, E0 contained VP4 and a pocket factor. Native RV-A2 RNA cores, obtained by gentle proteinase-K digestion in K and Na phosphate buffer, respectively, differed in accessibility of dsRNA regions, detected by PaSTRy. Variance in RNA compactness observed in K versus Na phosphate buffer was confirmed by rotary shadowing EM; in K phosphate buffer, the RNA remained condensed while, in Na phosphate buffer, distinct unfolding stages were apparent. PubMed: 41120457DOI: 10.1038/s41598-025-20627-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.2 Å) |
Structure validation
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