3PHP

STRUCTURE OF THE 3' HAIRPIN OF THE TYMV PSEUDOKNOT: PREFORMATION IN RNA FOLDING


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS 

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This is version 1.3 of the entry. See complete history


Literature

Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding.

Kolk, M.H.van der Graaf, M.Fransen, C.T.Wijmenga, S.S.Pleij, C.W.Heus, H.A.Hilbers, C.W.

(1998) EMBO J 17: 7498-7504

  • DOI: 10.1093/emboj/17.24.7498
  • Primary Citation of Related Structures:  
    3PHP

  • PubMed Abstract: 
  • The solution structure of an RNA-hairpin present in the pseudoknot, which is found at the 3'-terminus of turnip yellow mosaic virus genomic RNA, has been solved by nuclear magnetic resonance spectroscopy. The loop, which contains the sequence 5'-GGGUCA-3', was found to be highly structured and, contrary to expectations, does not attain its stability through GA or GC base pair formation but by triple interactions between the tilted adenosine and the minor groove sides of the first two guanosines ...

    The solution structure of an RNA-hairpin present in the pseudoknot, which is found at the 3'-terminus of turnip yellow mosaic virus genomic RNA, has been solved by nuclear magnetic resonance spectroscopy. The loop, which contains the sequence 5'-GGGUCA-3', was found to be highly structured and, contrary to expectations, does not attain its stability through GA or GC base pair formation but by triple interactions between the tilted adenosine and the minor groove sides of the first two guanosines. Interestingly, a very similar conformation was found for the cognate pseudoknot, implying that the 3'-hairpin is preformed for folding into a pseudoknotted structure. These findings suggest a mechanism of 'predetermined-fit' as a principle in RNA folding.


    Organizational Affiliation

    NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld, 6525 ED Nijmegen, The Netherlands.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*UP*UP*CP*CP*GP*AP*GP*GP*GP*UP*CP*AP*UP*CP*GP*GP*AP*AP*CP*CP*A) -3')A 23N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS 
  • OLDERADO: 3PHP Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-16
    Changes: Database references, Derived calculations