Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus


All retroviruses specifically package two copies of their genomes during virus assembly, a requirement for strand-transfer-mediated recombination during reverse transcription1,2. Genomic RNA exists in virions as dimers, and the overlap of RNA elements that promote dimerization and encapsidation suggests that these processes may be coupled3,4,5. Both processes are mediated by the nucleocapsid domain (NC) of the retroviral Gag polyprotein3. Here we show that dimerization-induced register shifts in base pairing within the Ψ-RNA packaging signal of Moloney murine leukaemia virus (MoMuLV) expose conserved UCUG elements that bind NC with high affinity (dissociation constant = 75 ± 12 nM). These elements are base-paired and do not bind NC in the monomeric RNA. The structure of the NC complex with a 101-nucleotide ‘core encapsidation’ segment of the MoMuLV Ψ site6 reveals a network of interactions that promote sequence- and structure-specific binding by NC's single CCHC zinc knuckle. Our findings support a structural RNA switch mechanism for genome encapsidation, in which protein binding sites are sequestered by base pairing in the monomeric RNA and become exposed upon dimerization to promote packaging of a diploid genome.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: MoMuLV Ψ site and structure of the NC–mΨCES complex.
Figure 2: Comparison of the guanosine binding sites of the MoMuLV and HIV-1 zinc knuckles.
Figure 3: NC binds to dimeric forms of DIS-1 and DIS-2.
Figure 4: Structural changes in the Ψ-site that seem to serve as a switch for the selective binding of NC to the dimer.

Similar content being viewed by others


  1. Varmus, H. E. Form and function of retroviral proviruses. Science 216, 812–820 (1982)

    Article  ADS  CAS  Google Scholar 

  2. Hu, W. S. & Temin, H. M. Retroviral recombination and reverse transcription. Science 250, 1227–1233 (1990)

    Article  ADS  CAS  Google Scholar 

  3. Prats, A.-C. et al. Cis elements and trans-acting factors involved in dimer formation of murine leukemia virus RNA. J. Virol. 64, 774–783 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Housset, V., De Rocquigny, H., Roques, B. P. & Darlix, J.-L. Basic amino acids flanking the zinc finger of Moloney murine leukemia virus nucleocapsid protein NCp10 are critical for virus infectivity. J. Virol. 67, 2537–2545 (1993)

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Paillart, J.-C., Shehu-Xhilaga, M., Marquet, R. & Mak, J. Dimerization of retroviral RNA genomes: an inseparable pair. Nature Rev. Microbiol. 2, 461–472 (2004)

    Article  CAS  Google Scholar 

  6. Mougel, M. & Barklis, E. A role for two hairpin structures as a core RNA encapsidation signal in murine leukemia virus virions. J. Virol. 71, 8061–8065 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Berkowitz, R., Fisher, J. & Goff, S. P. RNA packaging. Curr. Top. Microbiol. Immunol. 214, 177–218 (1996)

    CAS  PubMed  Google Scholar 

  8. Mann, R., Mulligan, R. C. & Baltimore, D. Construction of a retrovirus packaging mutant and its use to produce helper-free defective retrovirus. Cell 33, 153–159 (1983)

    Article  CAS  Google Scholar 

  9. Tounekti, N. et al. Effect of dimerization on the conformation of the encapsidation psi domain of Moloney murine leukemia virus RNA. J. Mol. Biol. 223, 205–220 (1992)

    Article  CAS  Google Scholar 

  10. Huthoff, H. & Berkhout, B. Two alternating structures of the HIV-1 leader RNA. RNA 7, 143–157 (2001)

    Article  CAS  Google Scholar 

  11. Oroudjev, E. M., Kang, P. C. E. & Kohlstaedt, L. A. An additional dimer linkage structure in Moloney murine leukemia virus RNA. J. Mol. Biol. 291, 603–613 (1999)

    Article  CAS  Google Scholar 

  12. Ly, H. & Parslow, T. G. Bipartite signal for genomic RNA dimerization in the Moloney murine leukemia virus. J. Virol. 76, 3135–3144 (2002)

    Article  CAS  Google Scholar 

  13. Kim, C.-H. & Tinoco, I. Jr. A retroviral RNA kissing complex containing only two G–C base pairs. Proc. Natl Acad. Sci. USA 97, 9396–9401 (2000)

    Article  ADS  CAS  Google Scholar 

  14. D'Souza, V. et al. Identification of a high-affinity nucleocapsid protein binding site within the Moloney murine leukemia virus Ψ-RNA packaging signal. Implications for genome recognition. J. Mol. Biol. 314, 217–232 (2001)

    Article  CAS  Google Scholar 

  15. D'Souza, V., Dey, A., Habib, D. & Summers, M. F. NMR structure of the 101 nucleotide core encapsidation signal of the Moloney murine leukemia virus. J. Mol. Biol. 337, 427–442 (2004)

    Article  CAS  Google Scholar 

  16. De Guzman, R. N. et al. Structure of the HIV-1 nucleocapsid protein bound to the SL3 Ψ-RNA recognition element. Science 279, 384–388 (1998)

    Article  ADS  CAS  Google Scholar 

  17. Amarasinghe, G. K. et al. NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the Ψ-RNA packaging signal. J. Mol. Biol. 301, 491–511 (2000)

    Article  CAS  Google Scholar 

  18. Schuller, W., Dong, C.-Z., Wecker, K. & Roques, B.-P. NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): Comparison with HIV-NCp7 complexes. Biochemistry 38, 12984–12994 (1999)

    Article  Google Scholar 

  19. Rein, A., Harvin, D. P., Mirro, J., Ernst, S. M. & Gorelick, R. J. Evidence that a central domain of nucleocapsid protein is required for RNA packaging in murine leukemia virus. J. Virol. 68, 6124–6129 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Bender, M. A., Palmer, T. D., Gelinas, R. E. & Miller, A. D. Evidence that the packaging signal of Moloney murine leukemia virus extends into the gag region. J. Virol. 61, 1639–1646 (1987)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Berkowitz, R. D., Ohagen, A., Hoglund, S. & Goff, S. P. Retroviral nucleocapsid domains mediate the specific recognition of genomic viral RNAs by chimeric Gag polyproteins during RNA packaging in vivo. J. Virol. 69, 6445–6456 (1995)

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Yang, S. & Temin, H. M. A double hairpin structure is necessary for the efficient encapsidation of spleen necrosis virus retroviral RNA. EMBO J. 13, 713–726 (1994)

    Article  CAS  Google Scholar 

  23. Hibbert, C. S., Mirro, J. & Rein, A. mRNA molecules containing MLV packaging signals are encapsidated as dimers. J. Virol. (in the press)

  24. Levin, J. G., Grimley, P. M., Ramseur, J. M. & Berezesky, I. K. Deficiency of 60 to 70S RNA in murine leukemia virus particles assembled in cells treated with actinomycin D. J. Virol. 14, 152–161 (1974)

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Sakuragi, J.-I., Shioda, T. & Panganiban, A. T. Duplication of the primary encapsidation and dimer linkage region of Human immunodeficiency virus type 1 RNA results in the appearance of monomeric RNA in virions. J. Virol. 75, 2557–2565 (2001)

    Article  CAS  Google Scholar 

  26. Torrent, C., Bordet, T. & Darlix, J.-L. Analytical study of rat retrotransposon VL30 RNA dimerization in vitro and packaging in murine leukemia virus. J. Mol. Biol. 240, 434–444 (1994)

    Article  CAS  Google Scholar 

  27. Méric, C. & Goff, S. P. Characterization of Moloney murine leukemia virus mutants with single-amino-acid substitutions in the Cys-His box of the nucleocapsid protein. J. Virol. 63, 1558–1568 (1989)

    PubMed  PubMed Central  Google Scholar 

  28. Antao, V. P., Lai, S. Y. & Tinoco, I. Jr. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19, 5901–5905 (1991)

    Article  CAS  Google Scholar 

  29. Wüthrich, K. NMR of Proteins and Nucleic Acids (John Wiley, New York, 1986)

    Book  Google Scholar 

  30. Kay, L. E., Clore, G. M., Bax, A. & Gronenborn, A. M. Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1β in solution. Science 249, 411–414 (1990)

    Article  ADS  CAS  Google Scholar 

Download references


We thank the HHMI staff and colleagues at UMBC for technical support. This research was supported by a grant from the NIH to M.F.S.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Michael F. Summers.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figures (DOC 2090 kb)

Supplementary Table

Statistical information associated with the structure calculations for the MLV NC-mCES complex (DOC 21 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

D'Souza, V., Summers, M. Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature 431, 586–590 (2004).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing