Structural View of Biology

Scroll to a Molecule of the Month Feature in this subcategory: Adenovirus Bacteriophage phiX174 Dengue Virus HIV-1 Protease Hemagglutinin Influenza Neuraminidase Integrase Parvoviruses Poliovirus and Rhinovirus Reverse Transcriptase Simian Virus 40 Tobacco Mosaic Virus

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  Adenovirus

  Viruses are one of the most dangerous enemies to our health, attacking cells and causing deadly diseases like AIDS and influenza. However, scientists are currently discovering ways to trick viruses into improving our health instead of causing disease. Adenovirus is one of the viruses being used in this work. It is found around the world, but it usually causes only mild disease when it infects cells. It can be life-threatening, however, in infants or people with weakened immune systems. Modified forms of the virus are being developed to cure genetic diseases, to fight cancer, and to deliver vaccines.
  
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  Discussed Structures

  

  adenovirus

  

  adenovirus
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  Bacteriophage phiX174

  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.
  
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  Discussed Structures

  

  bacteriophage phiX174 procapsid
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  Dengue Virus

  Dengue virus is a major threat to health in tropical countries around the world. It is limited primarily to the tropics because it is transmitted by a tropical mosquito, but even with this limitation, 50-100 million people are infected each year. Most infected people experience dengue fever, with terrible headaches and fever and rashes that last a week or two. In some cases, however, the virus weakens the circulatory system and can lead to deadly hemorrhaging. Researchers are now actively studying the virus to try to develop drugs to cure infection, and vaccines to block infection before it starts.
  
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  Discussed Structures

  

  dengue virus capsid

  

  dengue virus envelope glycoprotein

  

  dengue virus methyltransferase

  

  dengue virus methyltransferase

  

  dengue virus protease/helicase
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  HIV-1 Protease

  Drugs that attack HIV-1 protease are one of the triumphs of modern medicine. The AIDS epidemic started a few short decades ago-- before that, HIV was unknown. These drugs demonstrate the powerful tools that medical science has to combat a new disease. Already, researchers have discovered a panel of effective drugs which slow the growth of the virus to a standstill. Important problems still remain, however. In particular, an effective vaccine against HIV is not available. But today, HIV-infected individuals have potent options for treatment.
  
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  Discussed Structures

  

  HIV protease with a peptide-like inhibitor

  

  HIV protease with saquinavir
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  Hemagglutinin

  Influenza virus is a dangerous enemy. Normally, the immune system fights off infections, eradicating the viruses and causing a few days of miserable flu symptoms. Yearly flu vaccines prime our immune system, making it ready to fight the most common strains of influenza virus. But once every couple of decades, a new strain of influenza appears that is far more pathogenic, allowing it to spread rapidly. This happened at the end of World War I, and the resultant pandemic killed over 20 million people, more than twice the number of people that were killed in the war.
  
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  Discussed Structures

  

  hemagglutinin

  

  hemagglutinin

  

  hemagglutinin and antibodies
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  Influenza Neuraminidase

  Influenza virus is continually changing and every decade or so, a dangerous new strain appears and poses a threat to public health. This year, there has been an outbreak of a new strain of H1N1 flu, more commonly known as swine flu. The H1N1 designation refers to the two molecules that cover the surface of the virus: hemagglutinin and neuraminidase. Together, these two molecules control the infectivity of the virus. Hemagglutinin plays the starring role as the virus approaches a cell, binding to polysaccharide chains on the cell surface and then injecting the viral genome into the cell. Neuraminidase, on the other hand, plays its major role after the virus leaves an infected cell. It ensures that the virus doesn't get stuck on the cell surface by clipping off the ends of these polysaccharide chains.
  
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  Discussed Structures

  

  neuraminidase

  

  neuraminidase and sialic acid

  

  neuraminidase and antibodies
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  Integrase

  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.
  
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  Discussed Structures

  

  integrase target capture complex

  

  integrase strand transfer complex
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  Parvoviruses

  Viruses are finely tuned to perform their deadly job. Many viruses are highly specific: they infect only a particular animal or plant, and may even only infect a few types of cells within their preferred hosts. However, viruses occasionally cross the line, and gain the ability to infect other hosts. This is often termed viral emergence, and has been sensationalized as a major threat to global health in books such as The Hot Zone. Fortunately, this type of switching occurs only rarely, but when it does, it can be a disaster.
  
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  Discussed Structures

  

  feline panleukopenia virus (FPV)

  

  canine parvovirus

  

  B19 parvovirus
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  Poliovirus and Rhinovirus

  Viruses are biological hijackers. They attack a living cell and force it to make many new viruses, often destroying the cell in the process. Picornaviruses, or "little RNA viruses," are among the most simple viruses. They are composed of a modular protein shell, which seeks out and binds to a target cell surface, surrounding a short piece of RNA, which contains all of the information needed to co-opt the cell's machinery and direct the construction of new viruses. In spite of their simplicity, or perhaps because of it, the picornaviruses are also among the most important viruses for human health and welfare. Three familiar examples are shown here: poliovirus at the top (PDB entry 2plv), rhinovirus at the center (PDB entry 4rhv), and the virus that causes foot and mouth disease in livestock at the bottom (PDB entry 1bbt).
  
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  Discussed Structures

  

  poliovirus capsid

  

  rhinovirus capsid

  

  foot-and-mouth disease virus capsid

  

  rhinovirus bound to its cellular receptor
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  Reverse Transcriptase

  Viruses are tricky. They use all sorts of unusual mechanisms during their attacks on cells. HIV is no exception. It is a retrovirus, which means that it has the ability to insert its genetic material into the genome of the cells that it infects. But, infectious HIV particles carry their genome in RNA strands. Somehow, during infection, the virus needs to make a DNA copy of its RNA genome. This is very unusual, because all of the normal cellular machinery is designed to make RNA copies from DNA, but not the reverse. DNA is normally only created using other DNA strands as a template. This tricky reversal of synthesis is performed by the enzyme reverse transcriptase, shown here from PDB entry 3hvt. Inside its large, claw-shaped active site, it copies the HIV RNA and creates a double-stranded DNA version of the viral genome. This then integrates into the cell's DNA, and later instructs the cell to make additional copies of the virus.
  
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  Discussed Structures

  

  reverse transcriptase with DNA

  

  reverse transcriptase with nevirapine
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  Simian Virus 40

  Simian virus 40 is an example of how simple a virus can be and still perform its deadly job. Viruses are tiny machines with a single purpose: to reproduce themselves. They enter cells and hijack their synthetic machinery, forcing them to create new viruses. SV40 does this with very little molecular machinery. It is enclosed by a spherical capsid composed of 360 copies of one protein, seen in PDB entry 1sva, and a few copies of two others. This capsid is just big enough to enclose a small circle of DNA 5243 nucleotides long, which contains the barest minimum of information needed to get into the cell and make new viruses.
  
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  Discussed Structures

  

  SV40 capsid

  

  SV40 T-antigen

  

  SV40 T-antigen

  

  SV40 T-antigen
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  Tobacco Mosaic Virus

  Tobacco mosaic virus (TMV) has been at the center of virus research since its discovery over a hundred years ago. TMV was the first virus to be discovered. Late in the 19th century, researchers found that a tiny infectious agent, too small to be a bacterium, was the cause of a disease of tobacco plants. It then took 30 years of work before the nature of this mysterious agent became apparent. In a Nobel-prize-winning study, Wendell Stanley coaxed the virus to form crystals, and discovered that it was composed primarily of protein. Others quickly discovered that there was also RNA in the virus. Then, many prominent structural researchers (including J. D. Bernal, Rosalind Franklin, Ken Holmes, Aaron Klug, Don Caspar, and Gerald Stubbs) used X-ray diffraction and electron microscopy to probe the structure of the virus.
  
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  Discussed Structures

  

  tobacco mosaic virus

  

  tobacco mosaic virus disk