2DD2

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 27 
  • Selection Criteria: structures with the lowest energy, structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA

Chen, G.Kennedy, S.D.Qiao, J.Krugh, T.R.Turner, D.H.

(2006) Biochemistry 45: 6889-6903

  • DOI: 10.1021/bi0524464
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG ...

    A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.


    Organizational Affiliation

    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627, USA.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3'A10N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P))-3'B10N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 27 
  • Selection Criteria: structures with the lowest energy, structures with the least restraint violations 
  • OLDERADO: 2DD2 Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance