2RN1

Liquid crystal solution structure of the kissing complex formed by the apical loop of the HIV TAR RNA and a high affinity RNA aptamer optimized by SELEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 800 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

Van Melckebeke, H.Devany, M.Di Primo, C.Beaurain, F.Bryce, D.L.Boisbouvier, J.

(2008) Proc Natl Acad Sci U S A 105: 9210-9215

  • DOI: 10.1073/pnas.0712121105
  • Primary Citation of Related Structures:  
    2RN1

  • PubMed Abstract: 
  • Transactivation-response element (TAR) is a stable stem-loop structure of HIV RNA, which plays a crucial role during the life cycle of the virus. The apical loop of TAR acts as a binding site for essential cellular cofactors required for the replication of HIV ...

    Transactivation-response element (TAR) is a stable stem-loop structure of HIV RNA, which plays a crucial role during the life cycle of the virus. The apical loop of TAR acts as a binding site for essential cellular cofactors required for the replication of HIV. High-affinity aptamers directed against the apical loop of TAR have been identified by the SELEX approach. The RNA aptamers with the highest affinity for TAR fold as hairpins and form kissing complexes with the targeted RNA through loop-loop interactions. The aptamers with the strongest binding properties all possess a GA base pair combination at the loop-closing position. Using liquid-crystal NMR methodology, we have obtained a structural model in solution of a TAR-aptamer kissing complex with an unprecedented accuracy. This high-resolution structure reveals that the GA base pair is unilaterally shifted toward the 5' strand and is stabilized by a network of intersugar hydrogen bonds. This specific conformation of the GA base pair allows for the formation of two supplementary stable base-pair interactions. By systematic permutations of the loop-closing base pair, we establish that the identified atomic interactions, which form the basis for the high stability of the complex, are maintained in several other kissing complexes. This study rationalizes the stabilizing role of the loop-closing GA base pairs in kissing complexes and may help the development or improvement of drugs against RNA loops of viruses or pathogens as well as the conception of biochemical tools targeting RNA hairpins involved in important biological functions.


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph-Fourier, 41 Rue Jules Horowitz, F-38027 Grenoble, France.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*AP*GP*CP*CP*CP*UP*GP*GP*GP*AP*GP*GP*CP*UP*C)-3')A 16N/A
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*CP*UP*GP*GP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3')B 16N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 800 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2RN1 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations, Other