7EGQ

Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading

Summary for 7EGQ

• Entry DOI: 10.2210/pdb7egq/pdb
• EMDB information: 31138
• Descriptor: RNA-directed RNA polymerase, ZINC ION, MAGNESIUM ION, ... (11 entities in total)
• Functional Keywords: sars-cov-2, replication-transcription complex, nsp10 and nsp14, viral protein-rna complex, viral protein/rna
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV); More
• Total number of polymer chains: 22
• Total formula weight: 801369.78

Authors

Yan, L.M.,Yang, Y.X.,Li, M.Y.,Zhang, Y.,Zheng, L.T.,Ge, J.,Huang, Y.C.,Liu, Z.Y.,Wang, T.,Gao, S.,Zhang, R.,Huang, Y.Y.,Guddat, L.W.,Gao, Y.,Rao, Z.H.,Lou, Z.Y. (deposition date: 2021-03-25, release date: 2021-07-21, Last modification date: 2024-06-05)

Primary citation

Yan, L.,Yang, Y.,Li, M.,Zhang, Y.,Zheng, L.,Ge, J.,Huang, Y.C.,Liu, Z.,Wang, T.,Gao, S.,Zhang, R.,Huang, Y.Y.,Guddat, L.W.,Gao, Y.,Rao, Z.,Lou, Z.
Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading.
Cell, 184:3474-3485.e11, 2021

PubMed Abstract: The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) (GpppA) at 5' end of pre-mRNA. A dimeric form of Cap(0)-RTC observed by cryo-EM suggests an in trans backtracking mechanism for nsp14 ExoN to facilitate proofreading of the RNA in concert with polymerase nsp12. These results not only provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but also shed light on how replication fidelity in SARS-CoV-2 is maintained.

PubMed: 34143953
DOI: 10.1016/j.cell.2021.05.033

Experimental method

ELECTRON MICROSCOPY (3.35 Å)