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Three-dimensional structure determination with an X-ray laser
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. (Molecular biophysics)
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus. 

Keyword [en]
Mimivirus, flash diffraction, three dimensional, imaging, CXI
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-179597OAI: oai:DiVA.org:uu-179597DiVA: diva2:545328
EU, European Research Council
Available from: 2012-08-20 Created: 2012-08-20 Last updated: 2014-09-26
In thesis
1. Flash Diffractive Imaging in Three Dimensions
Open this publication in new window or tab >>Flash Diffractive Imaging in Three Dimensions
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers.

These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus.

We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient.

Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 68 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 960
X-ray, diffraction, mimivirus, three dimensional, phase retrieval, EMC, manifold embedding, CXI, FEL, free-electron laser, single particle
National Category
Research subject
Physics with specialization in Biophysics
urn:nbn:se:uu:diva-179643 (URN)978-91-554-8439-2 (ISBN)
Public defence
2012-10-05, B22, BMC, Husargatan 3, Uppsala, 09:15 (English)
Available from: 2012-09-14 Created: 2012-08-21 Last updated: 2013-01-22Bibliographically approved

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Ekeberg, TomasMaia, Filipe
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