2IRO

The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2

  • Classification: RNA

  • Deposited: 2006-10-16 Released: 2007-02-20 
  • Deposition Author(s): Tolbert, B.S.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR Structures of (rGCUGAGGCU)(2) and (rGCGGAUGCU)(2): Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs(,).

Tolbert, B.S.Kennedy, S.D.Schroeder, S.J.Krugh, T.R.Turner, D.H.

(2007) Biochemistry 46: 1511-1522

  • DOI: 10.1021/bi061350m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The NMR structures of [see text] and [see text] are reported. The internal loop, [see text], is about 2 kcal/mol more stable than [see text] at 37 degrees C. The duplexes assemble into similar global folds characterized by the formation of tandem she ...

    The NMR structures of [see text] and [see text] are reported. The internal loop, [see text], is about 2 kcal/mol more stable than [see text] at 37 degrees C. The duplexes assemble into similar global folds characterized by the formation of tandem sheared GA pairs. The different stabilities of the loops are accompanied by differences in the local structure of the closing GU pairs. In the [see text] internal loop, the GU pairs form canonical wobble configurations with two hydrogen bonds, whereas in [see text], the GU pairs form a single hydrogen bond involving the amino group, GH22, and the carbonyl group, UO4. This pairing is similar to the GU closing pair of the 690 hairpin loop found in E. coli 16S rRNA. The [see text] and [see text] structures reveal how the subtle interplay between stacking and hydrogen bonding determines sequence dependent conformation and thermodynamic stability. Thus, this work provides structural and thermodynamic benchmarks for theoreticians in the ongoing effort to understand the sequence dependence of RNA physicochemical properties.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3'A,B9N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-10-16 
  • Released Date: 2007-02-20 
  • Deposition Author(s): Tolbert, B.S.

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance