8VCI | pdb_00008vci

SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibranch Loop

• PDB DOI: https://doi.org/10.2210/pdb8VCI/pdb
• EM Map EMD-43137: EMDB EMDataResource
• NAKB: 8VCI

• Classification: RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): Yes 


• Deposited: 2023-12-14 Released: 2024-01-17 
• Deposition Author(s): Peterson, J.M., Becker, S.T., O'Leary, C.A., Juneja, P., Yang, Y., Moss, W.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop.

Peterson, J.M., Becker, S.T., O'Leary, C.A., Juneja, P., Yang, Y., Moss, W.N.

(2024) Biochemistry 63: 1287-1296

• PubMed: 38727003 
• DOI: https://doi.org/10.1021/acs.biochem.3c00716
• Primary Citation of Related Structures:  
  8VCI


• PubMed Abstract: 
  

  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshift stimulatory element (FSE) is necessary for programmed -1 ribosomal frameshifting (-1 PRF) and optimized viral efficacy. The FSE has an abundance of context-dependent alternate conformations, but two of the structures most crucial to -1 PRF are an attenuator hairpin and a three-stem H-type pseudoknot structure. A crystal structure of the pseudoknot alone features three RNA stems in a helically stacked linear structure, whereas a 6.9 Å cryo-EM structure including the upstream heptameric slippery site resulted in a bend between two stems. Our previous research alluded to an extended upstream multibranch loop that includes both the attenuator hairpin and the slippery site-a conformation not previously modeled. We aim to provide further context to the SARS-CoV-2 FSE via computational and medium resolution cryo-EM approaches, by presenting a 6.1 Å cryo-EM structure featuring a linear pseudoknot structure and a dynamic upstream multibranch loop.

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Organizational Affiliation: 

Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 37.9 kDa 
• Atom Count: 2,504 
• Modelled Residue Count: 118 
• Deposited Residue Count: 118 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Frameshift Stimulatory Element with Upstream Multi-branch Loop	A	118	Severe acute respiratory syndrome coronavirus 2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Peterson, J.M., Becker, S.T., O'Leary, C.A., Juneja, P., Yang, Y., Moss, W.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM133810

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Database references
• Version 1.2: 2024-05-29
  Changes: Database references