In a study published today in Nature, researchers at the Okinawa Institute of Science and Technology Graduate University (OIST) have for the first time imaged the structure of a central component of the Ebola virus at near-atomic resolution.
The researchers focused on a part of the virus called the nucleocapsid (NC), a complex of proteins that acts as a support structure for the viral genetic material. This structure allows the virus to replicate its deadly payload. They isolated nucleoprotein-RNA complexes, which make up the core of NCs, to a high degree of purity, then analyzed them with a cryo-electron microscope (cryo-EM) to take the closest-ever look at their structure.
"Before this study, we only knew about the smallest pieces of the NC structure," says primary author Dr. Yukihiko Sugita, "Now that we can see it as a whole, it may help find targets for antiviral drugs."
The complete Ebola virus has an invisible, filamentous structure that looks like a short strand of hair when magnified thousands of times. Inside these filaments are the pieces that make up a functioning virus: NC and matrix proteins, both of which are wrapped by surface glycoproteins and a viral envelope.
Previous studies had analyzed the NC structure using a technique called electron tomography, but the cryo-EM reconstruction generated by the OIST team has much higher definition, resolving individual RNA nucleotides and amino-acid side chains. "Our paper shows for the first time what the NC structure looks like at near-atomic resolution," says senior author Dr. Matthias Wolf.
It was a slow process achieving this picture, however. "The protein complexes are very fragile," Sugita says. "Getting a complete sample was very tricky."
Once the samples were prepared, it took the team more than 18 months to find just the right way to reconstruct the NC as a digital model. The helical structure of the protein complex is deceptively simple, but it has a fine complexity to it. But after a systematic search, a few hints provided by another team's publication, and new insight provided by their own high-resolution analysis, the OIST team's hard work paid off; everything slotted into place.
"Now that we have a clear picture of what this structure really looks like," says Wolf, "it is one step closer to figuring out how the whole virus works."
Image: Left: A 3D rendering of the cryo-EM reconstruction. The RNA and NP are colored in red and gray, respectively. A single NP molecule is highlighted in blue. Right: An atomic model of a single NP molecule with the RNA in the complex. The model is superposed with the cryo-EM map in a polygon mesh representation. Image courtesy of Yukihiko Sugita.