9FX9
CryoEM structure of RV-A89
Summary for 9FX9
| Entry DOI | 10.2210/pdb9fx9/pdb |
| EMDB information | 50844 |
| Descriptor | Capsid protein VP1, Capsid protein VP2, Capsid protein VP3 (3 entities in total) |
| Functional Keywords | rv-a89, rhinovirus, virus |
| Biological source | Human rhinovirus 89 ATCC VR-1199 More |
| Total number of polymer chains | 3 |
| Total formula weight | 76533.20 |
| Authors | Wald, J.,Goessweiner-Mohr, N.,Blaas, D.,Marlovits, T.C. (deposition date: 2024-07-02, release date: 2024-12-18) |
| Primary citation | Wald, J.,Goessweiner-Mohr, N.,Real-Hohn, A.,Blaas, D.,Marlovits, T.C. DMSO might impact ligand binding, capsid stability, and RNA interaction in viral preparations. Sci Rep, 14:30408-30408, 2024 Cited by PubMed Abstract: Dimethyl sulfoxide (DMSO) is a widely used solvent in drug research. However, recent studies indicate that even at low concentration DMSO might cause structural changes of proteins and RNA. The pyrazolopyrimidine antiviral OBR-5-340 dissolved in DMSO inhibits rhinovirus-B5 infection yet is inactive against RV-A89. This is consistent with our structural observation that OBR-5-340 is only visible at the pocket factor site in rhinovirus-B5 and not in RV-A89, where the hydrophobic pocket is collapsed. Here, we analyze the impact of DMSO in RV-A89 by high-resolution cryo-electron microscopy. Our 1.76 Å cryo-EM reconstruction of RV-A89 in plain buffer, without DMSO, reveals that the pocket-factor binding site is occupied by myristate and that the previously observed local heterogeneity at protein-RNA interfaces is absent. These findings suggest that DMSO elutes the pocket factor, leading to a collapse of the hydrophobic pocket of RV-A89. Consequently, the conformational heterogeneity observed at the RNA-protein interface in the presence of DMSO likely results from increased capsid flexibility due to the absence of the pocket factor and DMSO-induced affinity modifications. This local asymmetry may promote a directional release of the RNA genome during infection. PubMed: 39639094DOI: 10.1038/s41598-024-81789-x PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (1.96 Å) |
Structure validation
Download full validation report
