7EGQ image
Deposition Date 2021-03-25
Release Date 2021-07-21
Last Version Date 2025-07-02
Entry Detail
PDB ID:
7EGQ
Keywords:
VIRAL PROTEIN/RNA
Title:
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
Biological Source:
Source Organism:
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.35 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7EGQ validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA-directed RNA polymerase
Gene (Uniprot):rep
Chain IDs:A, I (auth: N)
Chain Length:932
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-structural protein 8
Gene (Uniprot):rep
Chain IDs:B, D, J (auth: O), L (auth: Q)
Chain Length:198
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-structural protein 7
Gene (Uniprot):rep
Chain IDs:C, K (auth: P)
Chain Length:83
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Helicase
Gene (Uniprot):rep
Chain IDs:E, M (auth: R), Q (auth: F), R (auth: S)
Chain Length:601
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-structural protein 9
Gene (Uniprot):rep
Chain IDs:F (auth: G), N (auth: T)
Chain Length:117
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Non-structural protein 10
Gene (Uniprot):rep
Chain IDs:G (auth: H), O (auth: U)
Chain Length:139
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Polymer Type:polyribonucleotide
Molecule:primer RNA
Chain IDs:S (auth: I), U (auth: L)
Chain Length:25
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polyribonucleotide
Molecule:Template RNA
Chain IDs:T (auth: J), V (auth: M)
Chain Length:33
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Proofreading exoribonuclease
Gene (Uniprot):rep
Chain IDs:H (auth: K), P (auth: X)
Chain Length:527
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087, PF08710, PF09401, PF06471 EC:2.7.7.48
Ligand Molecules
MG
ZN
Primary Citation
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)
PMID: 34143953 DOI: 10.1016/j.cell.2021.05.033

Abstact

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) (7MeGpppA) 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.

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Primary Citation of related structures
7EGQ
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