1F5U

SOLUTION STRUCTURE OF THE KISSING DIMER OF H3 GACG STEM-LOOP IN THE 5'-END DIMERIZATION SIGNAL OF MOLONEY MURINE LEUKEMIA VIRUS GENOMIC RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 19 
  • Conformers Submitted: 
  • Selection Criteria: averaged and energy-minimized structure based on 19 converged structures 

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This is version 1.4 of the entry. See complete history


Literature

A retroviral RNA kissing complex containing only two G.C base pairs.

Kim, C.H.Tinoco Jr., I.

(2000) Proc Natl Acad Sci U S A 97: 9396-9401

  • DOI: https://doi.org/10.1073/pnas.170283697
  • Primary Citation of Related Structures:  
    1F5U

  • PubMed Abstract: 

    The dimerization of viral RNA through noncovalent interactions at their 5' ends is a key step in the life cycle of retroviruses. In Moloney murine leukemia virus, three stem-loops are important in this process. One is a self-complementary tetraloop (H1), but the other two stem-loops (H2, H3) contain highly conserved GACG tetraloops that are not self-complementary sequences. Using two-dimensional NMR, we determined the structure of the H3 stem-loop. Surprisingly, it forms a stable, homodimeric kissing complex through only two intermolecular G small middle dotC base pairs. Cross-strand interactions of the adenines adjacent to the intermolecular G small middle dotC base pairs, plus unusual strong electrostatic interactions around the base pairs, contribute to the unexpected stability. This structure shows how even stem-loops without self-complementary sequences can facilitate the intermolecular recognition between two identical RNAs, and thus initiate dimerization and encapsidation of retroviral RNAs.


  • Organizational Affiliation

    Department of Chemistry, University of California, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley 94720-1460, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*UP*GP*GP*GP*AP*GP*AP*CP*GP*UP*CP*CP*CP*AP*CP*C)-3')
A, B
18N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 19 
  • Conformers Submitted: 
  • Selection Criteria: averaged and energy-minimized structure based on 19 converged structures 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection