scholarly journals SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction

2015 ◽  
Vol 190 (2) ◽  
pp. 200-214 ◽  
Author(s):  
Nicha C. Dvornek ◽  
Fred J. Sigworth ◽  
Hemant D. Tagare
Keyword(s):  
Single Particle ◽  
Maximum A Posteriori ◽  
A Posteriori ◽  
Single Particle Reconstruction ◽  
Particle Reconstruction

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

scholarly journals Development of Nanostructured Electron Microscopy Grids for Time Resolved Single Particle Reconstruction for Transmission Electron Microscopy

2006 ◽  
Vol 12 (S02) ◽  
pp. 1130-1131
Author(s):  
D Barnard ◽  
TR Shaikh ◽  
K Buttle ◽  
V Pushparaj ◽  
D Ye ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Single Particle ◽  
Time Resolved ◽  
Single Particle Reconstruction ◽  
Transmission Electron ◽  
Particle Reconstruction

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules

2010 ◽  
Vol 103 (1) ◽  
pp. 122-130 ◽  
Author(s):  
Kazuhiro Mio ◽  
Yuusuke Maruyama ◽  
Toshihiko Ogura ◽  
Masaaki Kawata ◽  
Toshio Moriya ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Single Particle ◽  
3D Structure ◽  
Single Particle Reconstruction ◽  
Particle Reconstruction

A Refined Single-Particle Reconstruction Procedure to Process Two-Dimensional Crystal Images from Transmission Electron Microscopy

2015 ◽  
Vol 21 (4) ◽  
pp. 876-885 ◽  
Author(s):  
Qie Kuang ◽  
Pasi Purhonen ◽  
Thirupathi Pattipaka ◽  
Yohannes H. Ayele ◽  
Hans Hebert ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Membrane Proteins ◽  
Single Particle ◽  
Three Dimensional ◽  
Reconstruction Procedure ◽  
Single Particle Reconstruction ◽  
Secondary Transporter ◽  
Unit Cells ◽  
2D Crystals ◽  
Particle Reconstruction

AbstractSingle-particle reconstruction (SPR) and electron crystallography (EC), two major applications in electron microscopy, can be used to determine the structure of membrane proteins. The three-dimensional (3D) map is obtained from separated particles in conventional SPR, but from periodic unit cells in EC. Here, we report a refined SPR procedure for processing 2D crystal images. The method is applied to 2D crystals of melibiose permease, a secondary transporter inEscherichia coli. The current procedure is improved from our previously published one in several aspects. The “gold standard Fourier shell correlation” resolution of our final reconstruction reaches 13 Å, which is significantly better than the previously obtained 17 Å resolution. The choices of different refinement parameters for reconstruction are discussed. Our refined SPR procedure could be applied to determine the structure of other membrane proteins in small or locally distorted 2D crystals, which are not ideal for EC.

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