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Left: A 3D rendering of cryo-EM reconstruction. RNA and NP are stained in red and gray, respectively. Only one molecule of NP is highlighted in blue. Right: An atomic model of a single molecule of NP with RNA in the complex. The model is superimposed on the cryo-EM map in a polygonal mesh representation. Credit: Yukihiko Sugita
Researchers from the Graduate University (OIST) of the Okinawa Institute of Science and Technology have for the first time imaged the structure of a central component of the Ebola virus at near-atomic resolution.
The study, published in the journal Nature, led by Prof. Dr. Matthias Wolf and lead author Dr. Yukihiko Sugita of OIST's Cryo-electron Molecular Microscopy Unit (MCEMU), in collaboration with world-renowned Professor Yoshihiro Kawaoka (virologist) ( University of Tokyo and University of Wisconsin-Madison), Takeshi Noda (Kyoto University) and Dr. Hideyuki Matsunami (OIST), a structural biologist.
The researchers focused on a part of the virus called nucleocapsid (NC), a protein complex that acts as a supporting structure for viral genetic material. This structure allows the virus to replicate its deadly payload, with a devastating effect. Dr. Sugita isolated with high purity the nucleoprotein-RNA complexes, which constitute the nucleus of NCs, and then analyzed them with a cryo-electron microscope (cryo-EM) to closely examine their structure.
"Before this study, we only knew the smallest parts of the NC structure," Dr. Sugita said. "Now that we can see it as a whole, it can help find targets for antiviral drugs."
The complete Ebola virus is a tiny, invisible filamentous structure that looks like a strand of hair when magnified thousands of times. Inside these filaments are the building blocks of a functional virus: NC and matrix proteins, both enveloped in surface glycoproteins and a viral envelope.
But neither the OIST scientists nor the public ran the risk of this study: the NP-RNA complex was produced without a real sequence of viral RNA in non-infectious cells grown in the OIST biosafety laboratory and did not present any risk. "It's like the parts of a car," said Professor Wolf, "unless the chassis, the engine, the wheels, etc. are all together, nothing works." C & # 39; is what the particle we have studied looks like – most of its components are absent, harmless. "
Previous studies had analyzed the NC structure with the help of a technique called electronic tomography, but the cryo-EM reconstruction generated by the OIST team has a much higher definition, solving the nucleotides of ## 147 ## 39, individual RNAs and side chains of amino acids. "Our article shows for the first time what the structure of the NC looks like at a near-atomic resolution," said Professor Wolf.
To get an idea of the progress of the team, imagine that you are watching your favorite movie. If the previous study looked like watching the film on a VHS tape, then its new structure looked like it was in a 4K presentation: the details are much sharper, with a clear definition that allows scientists to get an image the more detailed information about this component of the virus. .
However, the realization of this image has been slow. "The protein complexes are very fragile," said Dr. Sugita, "getting a full sample was very delicate."
Once the samples were prepared, it took more than 18 months for the team to find the right way to rebuild CN as a digital model. The helical structure of the protein complex is deceptively simple, but it has a fine complexity. Being on the precise number and symmetry by some of the tiny protein building blocks of the helix can invalidate the entire model. But after a systematic search, some clues provided by the publication of another team and a new analysis provided by their own high-resolution analysis, the hard work of the OIST team has borne fruit ; everything is in place.
"Now that we have a clear idea of what this structure really looks like," said Professor Wolf, "we have one more step to understand how the virus as a whole works."
The three-dimensional model generated from cryo-EM images provides a precise basis for future work. Researchers will now be able to conduct accurate targeted studies of the entire structure of the Ebola Virus Disease virus, which could indicate ways to defeat the virus.
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More information:
Yukihiko Sugita et al., Cryo-EM structure of the Ebola nucleoprotein-RNA complex at a resolution of 3.6 Å, Nature (2018). DOI: 10.1038 / s41586-018-0630-0
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