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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 97: 9396-9401

  • DOI: 10.1073/pnas.170283697
  • Also Cited By: 3CW1

  • 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 ( ...

    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
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*UP*GP*GP*GP*AP*GP*AP*CP*GP*UP*CP*CP*CP*AP*CP*C)-3')A,B18N/A
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

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance