8GWM
SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP
Summary for 8GWM
| Entry DOI | 10.2210/pdb8gwm/pdb |
| EMDB information | 34316 |
| Descriptor | RNA-directed RNA polymerase, 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate), Non-structural protein 8, ... (11 entities in total) |
| Functional Keywords | sars-cov-2, capping, nucleotide analogue inhibitor, cryo-em, viral protein, viral protein-inhibitor complex, viral protein/inhibitor |
| Biological source | Severe acute respiratory syndrome coronavirus 2 More |
| Total number of polymer chains | 9 |
| Total formula weight | 323942.60 |
| Authors | |
| Primary citation | Yan, L.,Huang, Y.,Ge, J.,Liu, Z.,Lu, P.,Huang, B.,Gao, S.,Wang, J.,Tan, L.,Ye, S.,Yu, F.,Lan, W.,Xu, S.,Zhou, F.,Shi, L.,Guddat, L.W.,Gao, Y.,Rao, Z.,Lou, Z. A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Cell, 185:4347-4360.e17, 2022 Cited by PubMed Abstract: Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs. PubMed: 36335936DOI: 10.1016/j.cell.2022.09.037 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.64 Å) |
Structure validation
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