Virtuelle (Nano) Welten PDB Molecule of the Month 103: Dengue Virus

Exploring the Structure

Cryoelectron microscopy has been used to study many aspects of the life cycle of the dengue virus. In these structures, a low resolution image of virus, not quite detailed enough to see atoms, is obtained by the electron microscope, and then atomic structures of the individual pieces are fit into the image to generate the final model. The one shown here, from PDB entry 2r6p, shows the envelope protein on the surface of the virus (in white) with many antibody Fab fragments (in blue) bound to the viral proteins. By looking carefully at this structure, researchers have discovered that the antibodies distort the arrangement of the envelope proteins, blocking their normal action in infection. Other dengue virus structures in the PDB include immature forms of the virus (for instance, in PDB entry 1n6g) and structures that include the membrane-spanning portions of the viral coat (PDB entry 1p58).

This illustration was created with Jmol--you can see an interactive version of the structure by clicking on the image. To see the scientific articles used for this Molecule of the Month and a few questions for further exploration, click here. Also available are related entries in the PDB as determined by a keyword search on June 23, 2008 for dengue virus.

Questions for Further Exploration

The dengue virus is surrounded by 180 copies of the envelope protein. Many other viruses are surrounded by capsids composed of many identical proteins, and these often appear in multiples of 60, such as 180, 240 or 420 copies. What is significant about these numbers? Can you find examples of each in the PDB?
Dengue virus is a member of a family of flaviviruses that are spread by ticks and mosquitoes. Other examples include yellow fever virus and West Nile virus. Looking at the structures in the PDB, can you see similarities in the proteins made by these viruses?
Dengue virus replicates in the cytoplasm of infected cells, without entering the nucleus. Can you think of any problems this might cause, and how the dengue virus solves them with its ten viral proteins?