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.

Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain


Short RNAs mediate gene silencing, a process associated with virus resistance, developmental control and heterochromatin formation in eukaryotes1,2,3,4,5. RNA silencing is initiated through Dicer-mediated processing of double-stranded RNA into small interfering RNA (siRNA)6,7. The siRNA guide strand associates with the Argonaute protein in silencing effector complexes, recognizes complementary sequences and targets them for silencing8,9,10,11. The PAZ domain is an RNA-binding module found in Argonaute and some Dicer proteins and its structure has been determined in the free state12,13,14. Here, we report the 2.6 Å crystal structure of the PAZ domain from human Argonaute eIF2c1 bound to both ends of a 9-mer siRNA-like duplex. In a sequence-independent manner, PAZ anchors the 2-nucleotide 3′ overhang of the siRNA-like duplex within a highly conserved binding pocket, and secures the duplex by binding the 7-nucleotide phosphodiester backbone of the overhang-containing strand and capping the 5′-terminal residue of the complementary strand. On the basis of the structure and on binding assays, we propose that PAZ might serve as an siRNA-end-binding module for siRNA transfer in the RNA silencing pathway, and as an anchoring site for the 3′ end of guide RNA within silencing effector complexes.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Overview of the PAZ–siRNA-like duplex structure.
Figure 2: The PAZ–siRNA-like duplex subcomplex.
Figure 3: The details of PAZ–siRNA-like duplex interaction.
Figure 4: RNA-binding assays monitored using surface plasmon resonance.


  1. Denli, A. M. & Hannon, G. J. RNAi: an ever-growing puzzle. Trends Biochem. Sci. 28, 196–201 (2003)

    CAS  Article  Google Scholar 

  2. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)

    CAS  Article  Google Scholar 

  3. Voinnet, O. RNA silencing as a plant immune system against viruses. Trends Genet. 17, 449–459 (2001)

    CAS  Article  Google Scholar 

  4. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002)

    ADS  CAS  Article  Google Scholar 

  5. Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002)

    ADS  CAS  Article  Google Scholar 

  6. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001)

    ADS  CAS  Article  Google Scholar 

  7. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001)

    CAS  Article  Google Scholar 

  8. Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000)

    ADS  CAS  Article  Google Scholar 

  9. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001)

    CAS  Article  Google Scholar 

  10. Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001)

    CAS  Article  Google Scholar 

  11. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002)

    CAS  Article  Google Scholar 

  12. Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468–474 (2003)

    ADS  Article  Google Scholar 

  13. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465–469 (2003)

    ADS  CAS  Article  Google Scholar 

  14. Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol. 10, 1026–1032 (2003)

    CAS  Article  Google Scholar 

  15. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001)

    CAS  Article  Google Scholar 

  16. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998)

    ADS  CAS  Article  Google Scholar 

  17. Chiu, Y. L. & Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034–1048 (2003)

    CAS  Article  Google Scholar 

  18. Theobald, D. L., Mitton-Fry, R. M. & Wuttke, D. S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32, 115–133 (2003)

    CAS  Article  Google Scholar 

  19. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921–1925 (2003)

    ADS  CAS  Article  Google Scholar 

  20. Hohjoh, H. RNA interference (RNAi) induction with various types of synthetic oligonucleotide duplexes in cultured human cells. FEBS Lett. 521, 195–199 (2002)

    CAS  Article  Google Scholar 

  21. Harborth, J. et al. Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev. 13, 83–105 (2003)

    CAS  Article  Google Scholar 

  22. Chiu, Y. L. & Rana, T. M. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol. Cell 10, 549–561 (2002)

    CAS  Article  Google Scholar 

  23. Holen, T., Amarzguioui, M., Wiiger, M. T., Babaie, E. & Prydz, H. Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res. 30, 1757–1766 (2002)

    CAS  Article  Google Scholar 

  24. Amarzguioui, M., Holen, T., Babaie, E. & Prydz, H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589–595 (2003)

    CAS  Article  Google Scholar 

  25. Czauderna, F. et al. Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res. 31, 2705–2716 (2003)

    CAS  Article  Google Scholar 

  26. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  27. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    CAS  Article  Google Scholar 

  28. Jones, T. & Kjeldgaard, M. Electron-density map interpretation. Methods Enzymol. 227, 174–208 (1997)

    Google Scholar 

  29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991)

    CAS  Article  Google Scholar 

  30. Katsamba, P. S., Park, S. & Laird-Offringa, I. A. Kinetic studies of RNA-protein interactions using surface plasmon resonance. Methods 26, 95–104 (2002)

    CAS  Article  Google Scholar 

Download references


We thank K. Saigo for providing us with the eIF2C1 complementary DNA clone. This research was supported by the NIH. We thank Y. Cheng and personnel at the Advanced Photon Source (APS) beamlines 19BM and 14IDB for help in collecting the X-ray diffraction data. Use of the APS beamline was supported by the US Department of Energy, Basic Energy Sciences, Office of Science.

Author information

Authors and Affiliations

Author notes

  1. Coordinates for the PAZ–siRNA complexes containing 2-nt ribo- and deoxyribonucleotide 3′ overhangs have been deposited in the Protein Data Bank under accession codes 1SI3 and 1SI2, respectively.

    • Keqiong Ye

Corresponding author

Correspondence to Dinshaw J. Patel.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Table 1

Crystallographic statistics (DOC 30 kb)

Supplementary Figure 1

Elution profiles of PAZ and PAZ-RNA complex. (JPG 26 kb)

Supplementary Figure 2

Stereo view of structural alignment of PAZ domains (JPG 62 kb)

Supplementary Figure 3

Sequence alignment of PAZ domains (JPG 172 kb)

Supplementary Figure Legends (DOC 26 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ma, JB., Ye, K. & Patel, D. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318–322 (2004).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

Further reading


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