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Keywords: retrovirus, retroviral lifecycle, DNA integration, HIV, AIDS, raltegravir


Retroviruses, such as HIV, are particularly insidious. Most viruses infect a cell, force it make many new copies of the virus, and then leave when the cell is used up. Retroviruses, however, take a long-term approach to infection. They enter cells and build a DNA copy of their genome. Then, they insert this viral genome into the cell's own DNA. This integrated DNA can be used immediately to build more viruses, or it can stay dormant, waiting for the best time to start virus production. This is one of the many reasons that HIV is so hard to fight: it can lie waiting in these long-lived cells for years.

DNA Integration

Integrase is the enzyme that splices the viral DNA into a cellular chromosome. Four identical copies of integrase grab the two ends of the viral DNA, creating a stable complex called an intasome. The intasome then binds to the cellular DNA and performs a strand transfer reaction, joining the viral DNA to the cellular DNA. The structure shown here (PDB entry 3os1) includes four integrase subunits (in blue) and three short pieces of DNA that correspond to the two viral DNA ends (red) and the cellular DNA (orange). The two integrase subunits at the center (light blue) provide the active sites that cut and join the DNA, and the outer pair of integrate subunits (dark blue) play a structural role.


Drugs Against HIV

Researchers have been studying HIV integrase for years, trying to understand how it works so that they can design drugs to fight AIDS. This work has led to the development of several effective drugs, including raltegravir, which is currently being used to treat HIV infection. So far, it has proven difficult to crystallize full-length HIV integrase and its complexes with DNA. The structures shown here are from a related retrovirus, prototype foamy virus (PFV). Although PFV is harmless, it is very similar to HIV integrase and provides an excellent model for studies of retroviral integration.


click on the above Jmol tab for an interactive visualization


Exploring the Structure

Structures of PFV integrase with DNA have revealed the critical steps of the integration reaction. The two Jmol images presented here show two different aspects of the structure. The first Jmol shows two structures: the complex just after the intasome captures the target DNA (PDB entry 3os1) and the complex after the strand transfer reaction (PDB entry 3os0). The second Jmol shows a close-up view of the active site with the drug raltegravir (magenta) bound to the two magnesium ions (green) that perform the reaction (PDB entry 3oya). The structure reveals that inhibitors like raltegravir bind in the active site and displace one end of the DNA strand.

Topics for further exploration

  1. You can use the Structure Comparison tool to compare the PFV integrase structures with the structures of different domains of HIV integrase.
  2. Structures of several inhibitors with PFV and HIV integrase are available in the PDB. You can use the Ligand Explorer (available in the asymmetric unit view) to look at the interaction of these inhibitors with the integrase active site.


  1. G. N. Maertens, S. Hare and P. Cherepanov (2010) The mechanism of retrovirual integration from X-ray structures of its key intermediates. Nature 468, 326-329.
  2. S. Hare, A. M. Vos, R. F. Clayton, J. W. Thuring, M. D. Cummings and P. Cherepanov (2010) Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Proceedings of the National Academy of Sciences USA 107, 20057-20062.
  3. M. Jackolski, J. N. Alexandratos, G. Bujacz and A. Wlodawer (2009) Piecing together the structure or retroviral integrase, and important target in AIDS therapy. FEBS Journal 276, 2926-2946.

Author Note

Entries included in Molecule of the Month articles are selected by the author, and do not represent a record of scientific priority or comprehensive review.

© 2015 David Goodsell & RCSB Protein Data Bank