2JSE

NMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

  • Classification: RNA

  • Deposited: 2007-07-03 Released: 2007-11-20 
  • Deposition Author(s): Shankar, N.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy and least distance and angle violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

NMR Reveals the Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA

Shankar, N., Xia, T., Kennedy, S.D., Krugh, T.R., Mathews, D.H., Turner, D.H.

(2007) Biochemistry 46: 12665-12678

  • DOI: 10.1021/bi700802s

  • PubMed Abstract: 

    • NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has ...

    NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics.

    Organizational Affiliation: 

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




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)-3')A22N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy and least distance and angle violations 

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-07-03 
  • Released Date: 2007-11-20 
  • Deposition Author(s): Shankar, N.

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance