scholarly journals High-resolution cryo-EM reconstructions in the presence of substantial aberrations

2019 ◽  
Author(s):  
Raquel Bromberg ◽  
Yirui Guo ◽  
Dominika Borek ◽  
Zbyszek Otwinowski
Keyword(s):  
High Resolution ◽  
Single Particle ◽  
Analytical Formula ◽  
Information Loss ◽  
Optical Aberrations ◽  
Shift Method ◽  
Single Particle Reconstruction ◽  
Beam Image ◽  
The Cost ◽  
Particle Reconstruction

The beam-image shift method accelerates data acquisition in cryo-EM single particle reconstruction (cryo-EM SPR) by fast repositioning of the imaging area, but at the cost of more severe and complex optical aberrations.We analyze here how uncorrected anti-symmetric aberrations, such as coma and trefoil, affect cryo-EM SPR results, and then infer an analytical formula quantifying information loss due to their presence that explains why Fourier-shell coefficient (FSC)-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. We validate our analysis with reference-based aberration refinement for two cryo-EM SPR datasets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and obtained 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively.Our results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher-order aberrations and address inconsistent guidelines regarding the level of aberrations acceptable in cryo-EM SPR experiments.

scholarly journals High-resolution cryo-EM reconstructions in the presence of substantial aberrations

IUCrJ ◽  
2020 ◽  
Vol 7 (3) ◽  
pp. 445-452 ◽  
Author(s):  
Raquel Bromberg ◽  
Yirui Guo ◽  
Dominika Borek ◽  
Zbyszek Otwinowski
Keyword(s):  
High Resolution ◽  
Single Particle ◽  
Analytical Formula ◽  
Information Loss ◽  
Higher Order ◽  
Data Sets ◽  
Higher Order Aberrations ◽  
Single Particle Reconstruction ◽  
Efficient Approach ◽  
Particle Reconstruction

Here, an analysis is performed of how uncorrected antisymmetric aberrations, such as coma and trefoil, affect cryo-EM single-particle reconstruction (SPR) results, and an analytical formula quantifying information loss owing to their presence is inferred that explains why Fourier-shell coefficient-based statistics may report significantly overestimated resolution if these aberrations are not fully corrected. The analysis is validated with reference-based aberration refinement for two cryo-EM SPR data sets acquired with a 200 kV microscope in the presence of coma exceeding 40 µm, and 2.3 and 2.7 Å reconstructions for 144 and 173 kDa particles, respectively, were obtained. The results provide a description of an efficient approach for assessing information loss in cryo-EM SPR data acquired in the presence of higher order aberrations, and address inconsistent guidelines regarding the level of aberrations that is acceptable in cryo-EM SPR experiments.

scholarly journals 3-D Structure of Cellulose Microfibril in Wood Using Electron Tomography and Single Particle Reconstruction Methods

2013 ◽  
Vol 19 (S2) ◽  
pp. 72-73
Author(s):  
M. Reza ◽  
P. Engelhardt ◽  
J. Ruokolainen
Keyword(s):  
Single Particle ◽  
Cellulose Microfibril ◽  
Electron Tomography ◽  
Single Particle Reconstruction ◽  
Reconstruction Methods ◽  
Particle Reconstruction

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

Single Particle Reconstruction of the Vault from TEP1 Knockout Mice and Refinement of the Computationally Selected Vault Barrel

2000 ◽  
Vol 6 (S2) ◽  
pp. 268-269
Author(s):  
P.L. Stewart ◽  
L.B. Kong ◽  
A.C. Siva ◽  
V.A. Kickhoefer ◽  
L. Harrington ◽  
...  
Keyword(s):  
Single Particle ◽  
Negative Influence ◽  
Cancer Drug ◽  
Molecular Architecture ◽  
Single Particle Reconstruction ◽  
Macromolecular Transport ◽  
Reconstruction Methods ◽  
Anti Cancer ◽  
Difference Imaging ◽  
Particle Reconstruction

The vault complex is a ubiquitous and predominantly cytoplasmic 13 MDa ribonucleoprotein assembly, composed of three proteins (TEP1, 240 kDa; VPARP, 193 kDa; and MVP, 100 kDa) and an untranslated RNA (vRNA) Although the basic cellular function of the vault is still unclear, recently it has been shown that induction of the major vault protein (MVP) has a direct negative influence on the nuclear uptake of the anti-cancer drug, doxorubicin. We have been applying cryo-EM single particle reconstruction methods to study the structure and molecular architecture of this cellular component. A published reconstruction of the intact rat vault at 31 Å resolution revealed that the complex is hollow and is structurally well suited to serve in macromolecular transport or sequestration. Higher resolution, 23 Å, was achieved for a reconstruction of the RNase-treated rat vault and difference imaging with the intact rat vault localized the vRNA to the ends of the vault caps.

scholarly journals SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs

2008 ◽  
Vol 3 (12) ◽  
pp. 1941-1974 ◽  
Author(s):  
Tanvir R Shaikh ◽  
Haixiao Gao ◽  
William T Baxter ◽  
Francisco J Asturias ◽  
Nicolas Boisset ◽  
...  
Keyword(s):  
Image Processing ◽  
Electron Micrographs ◽  
Single Particle ◽  
Biological Macromolecules ◽  
Single Particle Reconstruction ◽  
Particle Reconstruction

scholarly journals Extending the Limits of Single Particle Reconstruction

2009 ◽  
Vol 15 (S2) ◽  
pp. 566-567
Author(s):  
S Ludtke ◽  
M Schmid ◽  
W Chiu
Keyword(s):  
Single Particle ◽  
Single Particle Reconstruction ◽  
Particle Reconstruction

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

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