Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.02 kDa 
• Atom Count: 601 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

2AP0

Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures

• PDB DOI: 10.2210/pdb2AP0/pdb
• NDB: 2AP0

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-08-15 Released: 2006-09-05 
• Deposition Author(s): Cornish, P.V., Giedroc, D.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical

Cornish, P.V., Stammler, S.N., Giedroc, D.P.

(2006) RNA 12: 1959-1969

• PubMed: 17000902 
• DOI: 10.1261/rna.199006
• Primary Citation of Related Structures:  
  2AP0, 2AP5


• PubMed Abstract: 
  

The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
C27A Sugarcane Yellow Leaf Virus RNA pseudoknot	A	28	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2AP0 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-15 
• Released Date: 2006-09-05 
Deposition Author(s): Cornish, P.V., Giedroc, D.P.

Revision History  

• Version 1.0: 2006-09-05
  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: 2022-03-09
  Changes: Database references, Derived calculations