ISDA

Deposition Date 2021-07-12

Release Date 2021-11-24

Last Version Date 2025-05-14

Entry Detail

PDB ID:

7RDZ

Keywords:

REPLICATION/TRANSCRIPTION

Title:

SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - apo class

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-directed RNA polymerase
Gene (Uniprot):rep
Chain IDs:A
Chain Length:932
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087 EC:2.7.7.48

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Non-structural protein 8
Gene (Uniprot):rep
Chain IDs:B, D
Chain Length:199
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 EC:2.7.7.48

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Non-structural protein 7
Gene (Uniprot):rep
Chain IDs:C
Chain Length:88
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF06478, PF00680, PF08717, PF08716, PF20632, PF20633, PF20631, PF13087 EC:2.7.7.48

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Helicase
Gene (Uniprot):rep
Chain IDs:E, F
Chain Length:605
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 EC:2.7.7.48

Polymer Type:polyribonucleotide
Molecule:Product RNA
Chain IDs:G (auth: P)
Chain Length:35
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:Template RNA
Chain IDs:H (auth: T)
Chain Length:55
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

ADP

Primary Citation

Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.

Chen, J, Wang, Q, Malone, B, Llewellyn, E, Pechersky, Y, Maruthi, K, Eng, E.T, Perry, J.K, Campbell, E.A, Shaw, D.E, Darst, S.A, Chen, J, Wang, Q, Malone, B, Llewellyn, E, Pechersky, Y, Maruthi, K, Eng, E.T, Perry, J.K, Campbell, E.A, Shaw, D.E, Darst, S.A.Show

Nat.Struct.Mol.Biol. 29 250 260 (2022)

PMID: 35260847 DOI: 10.1038/s41594-022-00734-6

Abstact

The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex or RTC) associated with two copies of nsp13 (nsp132-RTC). One copy of nsp13 interacts with the template-RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here we use cryogenic-electron microscopy and molecular dynamics simulations to analyze the nsp132-RTC, revealing four distinct conformational states of the helicases. The results indicate a mechanism for the nsp132-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.

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Primary Citation of related structures