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PDBsum entry 2f4x
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RNA PDB id
2f4x

 

 

 

 

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Contents
DNA/RNA
PDB id:
2f4x
Name: RNA
Title: Nmr solution of HIV-1 lai kissing complex
Structure: 5'-r(p Gp Gp Up Up Gp Cp Up Gp Ap Ap Gp Cp Gp Cp Gp Cp Ap C p Gp Gp Cp Ap Ap C)-3'. Chain: a, b. Engineered: yes. Other_details: HIV-1 lai packaging signal
Source: Synthetic: yes. Other_details: RNA was prepared by in vitro transcription with t7 RNA polymerase
NMR struc: 18 models
Authors: F.Kieken,F.Paquet,F.Brule,J.Paoletti,G.Lancelot
Key ref: F.Kieken et al. (2006). A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer. Nucleic Acids Res, 34, 343-352. PubMed id: 16410614
Date:
24-Nov-05     Release date:   28-Feb-06    
 Headers
 References

DNA/RNA chains
  G-G-U-U-G-C-U-G-A-A-G-C-G-C-G-C-A-C-G-G-C-A-A-C 24 bases
  G-G-U-U-G-C-U-G-A-A-G-C-G-C-G-C-A-C-G-G-C-A-A-C 24 bases

 

 
Nucleic Acids Res 34:343-352 (2006)
PubMed id: 16410614  
 
 
A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer.
F.Kieken, F.Paquet, F.Brulé, J.Paoletti, G.Lancelot.
 
  ABSTRACT  
 
Dimerization of genomic RNA is directly related with the event of encapsidation and maturation of the virion. The initiating sequence of the dimerization is a short autocomplementary region in the hairpin loop SL1. We describe here a new solution structure of the RNA dimerization initiation site (DIS) of HIV-1(Lai). NMR pulsed field-gradient spin-echo techniques and multidimensional heteronuclear NMR spectroscopy indicate that this structure is formed by two hairpins linked by six Watson-Crick GC base pairs. Hinges between the stems and the loops are stabilized by intra and intermolecular interactions involving the A8, A9 and A16 adenines. The coaxial alignment of the three A-type helices present in the structure is supported by previous crystallography analysis but the A8 and A9 adenines are found in a bulged in position. These data suggest the existence of an equilibrium between bulged in and bulged out conformations in solution.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20825656 N.Ristic, and M.P.Chin (2010).
Mutations in matrix and SP1 repair the packaging specificity of a Human Immunodeficiency Virus Type 1 mutant by reducing the association of Gag with spliced viral RNA.
  Retrovirology, 7, 73.  
19460437 H.W.Lee, K.T.Briggs, and J.P.Marino (2009).
Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence.
  Methods, 49, 118-127.  
  19529749 M.D.Moore, and W.S.Hu (2009).
HIV-1 RNA dimerization: It takes two to tango.
  AIDS Rev, 11, 91.  
19452632 P.T.Li, and I.Tinoco (2009).
Mechanical unfolding of two DIS RNA kissing complexes from HIV-1.
  J Mol Biol, 386, 1343-1356.  
18996893 I.Lebars, P.Legrand, A.Aimé, N.Pinaud, S.Fribourg, and C.Di Primo (2008).
Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance.
  Nucleic Acids Res, 36, 7146-7156.
PDB code: 2jlt
18412127 J.Sarzyńska, K.Réblová, J.Sponer, and T.Kuliński (2008).
Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.
  Biopolymers, 89, 732-746.  
18008323 S.Mazier, and D.Genest (2008).
Insight into the intrinsic flexibility of the SL1 stem-loop from genomic RNA of HIV-1 as probed by molecular dynamics simulation.
  Biopolymers, 89, 187-196.  
17341460 A.Mujeeb, N.B.Ulyanov, S.Georgantis, I.Smirnov, J.Chung, T.G.Parslow, and T.L.James (2007).
Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding.
  Nucleic Acids Res, 35, 2026-2034.  
17768146 I.Lebars, T.Richard, C.Di Primo, and J.J.Toulmé (2007).
NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer.
  Nucleic Acids Res, 35, 6103-6114.
PDB codes: 2oom 2pn9
17466332 K.B.Turner, N.A.Hagan, and D.Fabris (2007).
Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein.
  J Mol Biol, 369, 812-828.  
17704156 K.Réblová, E.Fadrná, J.Sarzynska, T.Kulinski, P.Kulhánek, E.Ennifar, J.Koca, and J.Sponer (2007).
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.
  Biophys J, 93, 3932-3949.  
17267488 M.D.Moore, W.Fu, O.Nikolaitchik, J.Chen, R.G.Ptak, and W.S.Hu (2007).
Dimer initiation signal of human immunodeficiency virus type 1: its role in partner selection during RNA copackaging and its effects on recombination.
  J Virol, 81, 4002-4011.  
17070549 N.A.Hagan, and D.Fabris (2007).
Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1.
  J Mol Biol, 365, 396-410.  
16679451 E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.M.Weibel, A.M.Aubertin, P.Pale, P.Dumas, and R.Marquet (2006).
Targeting the dimerization initiation site of HIV-1 RNA with aminoglycosides: from crystal to cell.
  Nucleic Acids Res, 34, 2328-2339.
PDB codes: 2fcx 2fcy 2fcz 2fd0
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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