Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.00 kDa 
• Atom Count: 599 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

1YG4

Solution Structure of the ScYLV P1-P2 Frameshifting Pseudoknot, Regularized Average Structure

• PDB DOI: 10.2210/pdb1YG4/pdb
• NDB: 1YG4
• BMRB: 6509

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-01-04 Released: 2005-12-13 
• Deposition Author(s): Cornish, P.V., Hennig, M., Giedroc, D.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 1 
• Selection Criteria: averaged structure 

Literature

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting

Cornish, P.V., Hennig, M., Giedroc, D.P.

(2005) Proc Natl Acad Sci U S A 102: 12694-12699

• PubMed: 16123125 
• DOI: 10.1073/pnas.0506166102
• Primary Citation of Related Structures:  
  1YG3, 1YG4


• PubMed Abstract: 
  

The molecular determinants of stimulation of -1 programmed ribosomal frameshifting (-1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes -1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3' nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2'-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2'-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of -1 PRF (15 +/- 2%) relative to the BWYV pseudoknot (6 +/- 1%), a difference traced largely to the identity of the 3' nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by approximately 1.5 kcal x mol(-1) (pH 7.0, 37 degrees C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, TX 77843-2128, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ScYLV RNA pseudoknot	A	28	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 1 
• Selection Criteria: averaged structure 
• OLDERADO: 1YG4 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-04 
• Released Date: 2005-12-13 
Deposition Author(s): Cornish, P.V., Hennig, M., Giedroc, D.P.

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations