7L1F

SARS-CoV-2 RdRp in complex with 4 Remdesivir monophosphate

• PDB DOI: https://doi.org/10.2210/pdb7L1F/pdb
• NAKB: 7L1F
• EM Map EMD-23109: EMDB EMDataResource

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-14 Released: 2021-02-10 
• Deposition Author(s): Bravo, J.P.K., Taylor, D.W.
• Funding Organization(s): Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication.

Bravo, J.P.K., Dangerfield, T.L., Taylor, D.W., Johnson, K.A.

(2021) Mol Cell 81: 1548-1552.e4

• PubMed: 33631104 
• DOI: https://doi.org/10.1016/j.molcel.2021.01.035
• Primary Citation of Related Structures:  
  7L1F


• PubMed Abstract: 
  

  Remdesivir is a nucleoside analog approved by the US FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryo-EM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of 3 copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of 3 bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.

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Organizational Affiliation: 

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 134.21 kDa 
• Atom Count: 8,825 
• Modelled Residue Count: 1,044 
• Deposited Residue Count: 1,110 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A	898	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B [auth C]	114	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C [auth D]	63	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*UP*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*U*(F86)*(F86)*(F86)*(F86))-3')	D [auth P]	17	Severe acute respiratory syndrome coronavirus 2

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*UP*CP*UP*UP*AP*G)-3')	E [auth T]	18	Severe acute respiratory syndrome coronavirus 2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.89 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Bravo, J.P.K., Taylor, D.W.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	F-1938
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138348

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations