1PJY

Solution structure of the HIV-1 frameshift inducing stem-loop RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the HIV-1 frameshift inducing stem-loop RNA.

Staple, D.W.Butcher, S.E.

(2003) Nucleic Acids Res. 31: 4326-4331


  • PubMed Abstract: 
  • The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence ...

    The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed -1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem-loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem-loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 A] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem-loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A-A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HIV-1 frameshift inducing stem-loopA22N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance