2KY0

The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.

Hammond, N.B.Tolbert, B.S.Kierzek, R.Turner, D.H.Kennedy, S.D.

(2010) Biochemistry 49: 5817-5827

  • DOI: 10.1021/bi100332r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of mo ...

    Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)(2), (rGACUAGAGUCA)(2), (rGACAAGUGUCA)(2), (rGGUAGGCCA)(2), and (rGACGAGUGUCA)(2). The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC)(2) (Wu, M., SantaLucia, J., Jr., and Turner, D. H. (1997) Biochemistry 36, 4449-4460). For loops bounded by Watson-Crick pairs, the AG and Watson-Crick pairs are all head-to-head imino-paired (cis Watson-Crick/Watson-Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen-bonding interactions. Of the two loops bounded by G-U pairs, only the 5'UAGG/3'GGAU loop adopts canonical UG wobble pairing (cis Watson-Crick/Watson-Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5'GAGU/3'UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA)(2)) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson-Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in a dynamic or stacked conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3'A,B11N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance