1KIS

TAR-TAR "KISSING" HAIRPIN COMPLEX DERIVED FROM THE HIV GENOME, NMR, 1 STRUCTURE


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement.

Chang, K.Y.Tinoco Jr., I.

(1997) J Mol Biol 269: 52-66

  • DOI: 10.1006/jmbi.1997.1021
  • Primary Citation of Related Structures:  
    1KIS

  • PubMed Abstract: 
  • We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA "kissing" hairpin complex formed between the HIV-2 TAR hairpin loop and a hairpin with a complementary loop sequence. Kissing hairpins are important in natural antisense reactions; their complex is a specific target for protein binding ...

    We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA "kissing" hairpin complex formed between the HIV-2 TAR hairpin loop and a hairpin with a complementary loop sequence. Kissing hairpins are important in natural antisense reactions; their complex is a specific target for protein binding. The complex has all six nucleotides of each loop paired to form a bent quasicontinuous helix of three coaxially stacked helices: two stems plus a loop-loop interaction helix. Experimental constraints derived from heteronuclear and homonuclear NMR data on 13C and 15N-labeled RNA led to a structure for the loop-loop helix with an average root-mean-square deviation of 0.83 (+/-0.10) A for 33 converged structures relative to the average structure. The loop-loop helix of the kissing complex is distorted compared to A-form RNA. Its major groove is blocked by the phosphodiester bonds that connect the first loop residue of each hairpin with its own stem, and it is flanked by two negatively charged phosphate clusters. The loop-loop helix has alternating helical twists between adjacent base-pairs. The base-pairs at the helix junctions are overwound and three base-pairs near the helix junctions adopt high propeller twists. All these changes reduce the distance needed for the bridging phosphodiester bonds connecting each stem and loop to cross the major groove of the loop-loop helix, and result in a deformed RNA helix with localized perturbations in the minor groove surface. The alternating helical twist pattern, plus other distortions in the loop-loop helix may be important for Rom protein recognition of the kissing hairpin complex.


    Related Citations: 
    • Characterization of a "Kissing" Hairpin Complex Derived from the Human Immunodeficiency Virus Genome
      Chang, K.Y., Tinoco Jr, I.
      (1994) Proc Natl Acad Sci U S A 91: 8705

    Organizational Affiliation

    Department of Chemistry, University of California at Berkeley, 94720-1460, USA.



Macromolecules

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

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

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 17 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1KIS Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary