Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.45 kDa 
• Atom Count: 427 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

2RPT

Structure of the CC mismatch from the thymidylate synthase binding site 1 hairpin and analysis of its interaction with paromomycin

• PDB DOI: 10.2210/pdb2RPT/pdb
• NDB: 2RPT

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-08-23 Released: 2009-08-25 
• Deposition Author(s): Tavares, T.J., Johnson, P.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin

Tavares, T.J., Beribisky, A.V., Johnson, P.E.

(2009) RNA 15: 911-922

• PubMed: 19329536 
• DOI: 10.1261/rna.1514909
• Primary Citation of Related Structures:  
  2RPT


• PubMed Abstract: 
  

The structure of a cytosine-cytosine (CC) mismatch-containing RNA molecule derived from a hairpin structure in the thymidylate synthase mRNA that binds the aminoglycoside paromomycin with high affinity was determined using nuclear magnetic resonance (NMR) spectroscopy. The cytosines in the mismatch form a noncanonical base pair where both cytosines are uncharged and stack within the stem of the RNA structure. Binding to paromomycin was analyzed using isothermal titration calorimetry (ITC) to demonstrate the necessity of the CC mismatch and to determine the affinity dissociation constant of this RNA to paromomycin to be 0.5 +/- 0.3 microM. The CC mismatch, and the neighboring GC base pairs experienced the highest degree of chemical shift changes in their H6 and H5 resonances indicating that paromomycin binds in the major groove at the CC mismatch site. In comparing the structure of CC mismatch RNA with a fully Watson-Crick GC base paired stem, the CC mismatch is shown to confer a widening of the major groove. This widening, combined with the dynamic nature of the CC mismatch, enables binding of paromomycin to this RNA molecule.

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Organizational Affiliation: 

Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*CP*CP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*CP*GP*GP*CP*C)-3')	A	20	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2RPT Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-23 
• Released Date: 2009-08-25 
Deposition Author(s): Tavares, T.J., Johnson, P.E.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations