1TBK | pdb_00001tbk

NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.

• PDB DOI: https://doi.org/10.2210/pdb1TBK/pdb
• NAKB: 1TBK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2004-05-20 Released: 2005-03-01 
• Deposition Author(s): Campbell, D.O., Legault, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 61 
• Conformers Submitted: 11 
• Selection Criteria: The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11) 

Literature

Nuclear Magnetic Resonance Structure of the Varkud Satellite Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping

Campbell, D.O., Legault, P.

(2005) Biochemistry 44: 4157-4170

• PubMed: 15766243 
• DOI: https://doi.org/10.1021/bi047963l
• Primary Citation Related Structures: 
  1TBK


• PubMed Abstract: 
  

  An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.42 kDa 
• Atom Count: 358 
• Modeled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
VS ribozyme stem-loop V	A	17	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 61 
• Conformers Submitted: 11 
• Selection Criteria: The submitted conformer models are the 10 structures with the lowest energy (MODEL 2 -- 11) 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Campbell, D.O., Legault, P.

Revision History  

• Version 1.0: 2005-03-01
  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
• Version 1.4: 2024-05-22
  Changes: Data collection