A Milestone at the PDB

The 10,000th entry in the Protein Data Bank, the bacteriophage phiX174, is a perfect example of how the science of protein structure has progressed in four decades. In 1960, the world got its first look at the structure of a protein. That first structure was the small protein myoglobin, composed of one protein chain and one heme group--about 1260 atoms in all. By contrast, the 10,000th entry in the PDB contains 420 protein chains and over half a million atoms. Enormous structures like this are not uncommon in the Protein Data Bank. The stakes have risen dramatically since the structure of myoglobin was first revealed.

Animal, Mineral, or Vegetable?

A bacteriophage is a virus that attacks bacteria. The phiX174 bacteriophage attacks the common human bacteria Escherichia coli, infecting the cell and forcing it to make new viruses. Do you think that viruses are living organisms? PhiX174 is composed of a single circle of DNA surrounded by a shell of proteins. That's all. It can inject its DNA into a bacterial cell, then force the cell to create many new viruses. These viruses then burst out of the cell, and go on to hijack more bacteria. By itself, it is like an inert rock. But given the proper bacterial host, it is a powerful reproducing machine. What do you think? Is it alive?

A Molecular Time Bomb

The capsid of phiX174 is designed to find bacterial cells, and then infect them with its DNA. Sixty copies of the capsid protein (colored red here) form a spherical shell around the DNA, and the spike proteins (colored orange here) form 12 pentagonal spikes on the surface. It is thought that the DNA is ejected through the middle of the spikes when the virus infects an Escherichia coli cell. The DNA itself encodes 11 genes. In order to fit into this tiny protein shell, however, the DNA is so short that the genes must actually overlap.

Assembling a Virus

As one can imagine, assembling 120 protein chains into a perfect symmetrical shell is a difficult task. PhiX174 uses special scaffolding proteins to ensure that everything ends up in the right place. The capsid and spike proteins spontaneously form pentagonal units, with five copies of each chain. The scaffolding proteins (shown here in light blue and purple) then arrange these pentagon building-blocks into the whole icosahedron, complete with DNA inside. The scaffolding proteins are small, and bind to the inner and outer surfaces of the pentagons, aligning them one next to the other in the proper orientation.

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The DNA Inside

PhiX174 has the distinction of being the first organism for which a full genome sequence was determined. The virus contains one piece of DNA, 5386 bases long, wrapped into a small circle. In the mature virus, this small circle of DNA is packaged inside the icosahedral protein shell, safe for delivery to an unfortunate bacterial target. The PDB entry 1cd3 includes atomic coordinates for the capsid proteins, but the DNA inside is not included. It does not conform to the beautiful icosahedral symmetry of the capsid, and thus cannot be resolved by x-ray crystallography. We must imagine it packed inside, trapped as the last pentamer closes the capsid.

Exploring the Structure

You can easily look at one of the subunits of this bacteriophage. There are seven separate chains in the PDB file 1cd3. The spike protein, chain G, is small and compact and the capsid protein, chain F, is large. Both are very stable structures composed of two beta-sheets, forming a structure commonly called a "beta-sandwich." The ribbon diagram shows the chain of the spike protein. Notice how the beta-strands, each depicted with an arrow, arrange side-by-side to form the two sheets. Beta-sandwich structures like this are found in many different viruses.

Four copies of a small scaffolding protein (chains 1, 2, 3 and 4) are arranged in the angle between the capsid and spike proteins, ending up on the outside of the final virus capsid. Another small scaffold protein (chain B) is found on the inside of the capsid, where it assists in the capture of DNA. Compare this detailed atomic view of one subunit of the capsid to the picture of the whole capsid shown on the previous pages, which contains 60 identical copies of each of these seven proteins.

The pictures were created with RasMol. You can create similar pictures by accessing the PDB file 1cd3 and then clicking "View Structure."

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© 2013 David Goodsell & RCSB Protein Data Bank