6XRZ

The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome.

Zhang, K.Zheludev, I.N.Hagey, R.J.Wu, M.T.Haslecker, R.Hou, Y.J.Kretsch, R.Pintilie, G.D.Rangan, R.Kladwang, W.Li, S.Pham, E.A.Bernardin-Souibgui, C.Baric, R.S.Sheahan, T.P.D Souza, V.Glenn, J.S.Chiu, W.Das, R.

(2020) bioRxiv 

  • DOI: https://doi.org/10.1101/2020.07.18.209270
  • Primary Citation of Related Structures:  
    6XRZ

  • PubMed Abstract: 

    Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome 1, 2 . The frameshift stimulation element (FSE) of the SARS-CoV-2 genome is required for balanced expression of essential viral proteins and is highly conserved, making it a potential candidate for antiviral targeting by small molecules and oligonucleotides 3-6 . To aid global efforts focusing on SARS-CoV-2 frameshifting, we report exploratory results from frameshifting and cellular replication experiments with locked nucleic acid (LNA) antisense oligonucleotides (ASOs), which support the FSE as a therapeutic target but highlight difficulties in achieving strong inactivation. To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve 7 pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA nanostructure tagging method. This is the smallest macromolecule (88 nt; 28 kDa) resolved by single-particle cryo-EM at subnanometer resolution to date. The tertiary structure model, defined to an estimated accuracy of 5.9 Å, presents a topologically complex fold in which the 5' end threads through a ring formed inside a three-stem pseudoknot. Our results suggest an updated model for SARS-CoV-2 frameshifting as well as binding sites that may be targeted by next generation ASOs and small molecules.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome88Severe acute respiratory syndrome coronavirus 2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD021600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AI148382
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129564
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01AI120943
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122579

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references