1M5L

Structure of wild-type and mutant internal loops from the SL-1 domain of the HIV-1 packaging signal


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: 14 structures with the least restraint violations and the lowest energy; 1 ENERGY-MINIMIZED AVERAGE OF THE 14 CONVERGED STRUCTURES 

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This is version 1.4 of the entry. See complete history


Literature

Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal

Greatorex, J.Gallego, J.Varani, G.Lever, A.

(2002) J Mol Biol 322: 543-557

  • DOI: https://doi.org/10.1016/s0022-2836(02)00776-3
  • Primary Citation of Related Structures:  
    1M5L

  • PubMed Abstract: 

    The packaging signal (Psi) of the human immunodeficiency virus type 1 (HIV-1) enables encapsidation of the full-length genomic RNA against a background of a vast excess of cellular mRNAs. The core HIV-1 Psi is approximately 109 nucleotides and contains sequences critical for viral genomic dimerisation and splicing, in addition to the packaging signal. It consists of a series of stem-loops (termed SL-1 to SL-4), which can be arranged in a cloverleaf secondary structure. Using a combination of NMR spectroscopy, UV melting experiments, molecular modeling and phylogenetic analyses, we have explored the structure of two conserved internal loops proximal to the palindromic sequence of SL-1. Internal loop A, composed of six purines, forms a flexible structure that is strikingly similar to the Rev responsive element motif when bound to Rev protein. This result suggests that it may function as a protein-binding site. The absolutely conserved four-purine internal loop B is instead conformationally and thermodynamically unstable, and exhibits multiple conformations in solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G base-triplet. The structure of the GGA mutant explains the relative instability of the wild-type loop. In a manner analogous to SL-3, we propose that conformational flexibility at this site may facilitate melting of the structure during Gag protein capture or genomic RNA dimerisation.


  • Organizational Affiliation

    Department of Medicine, University of Cambridge, Level 5, Addenbrookes Hospital, Hills Road, CB2 2QQ, Cambridge, UK.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
modified HIV-1 packaging signal stem-loop 1 RNA38N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: 14 structures with the least restraint violations and the lowest energy; 1 ENERGY-MINIMIZED AVERAGE OF THE 14 CONVERGED STRUCTURES 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection