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Literature DB >> 18926912

JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.

Junjie Zhang¹, Natsuko Nakamura, Yuko Shimizu, Nathan Liang, Xiangan Liu, Joanita Jakana, Michael P Marsh, Christopher R Booth, Takao Shinkawa, Munetaka Nakata, Wah Chiu.

Abstract

The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure.

Entities: CellLine Chemical Disease Species

Mesh：

Substances：
Ice

Year: 2008 PMID： 18926912 PMCID： PMC2634810 DOI： 10.1016/j.jsb.2008.09.006

Source DB: PubMed Journal: J Struct Biol ISSN： 1047-8477 Impact factor: 2.867

25 in total

1. Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope.

Authors: Jianlin Lei; Joachim Frank
Journal: J Struct Biol Date: 2005-04 Impact factor: 2.867

2. Modular software platform for low-dose electron microscopy and tomography.

Authors: Michael P Marsh; Juan T Chang; Christopher R Booth; Nathan L Liang; Michael F Schmid; Wah Chiu
Journal: J Microsc Date: 2007-12 Impact factor: 1.758

3. De novo backbone trace of GroEL from single particle electron cryomicroscopy.

Authors: Steven J Ludtke; Matthew L Baker; Dong-Hua Chen; Jiu-Li Song; David T Chuang; Wah Chiu
Journal: Structure Date: 2008-03 Impact factor: 5.006

4. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.

Authors: Wen Jiang; Matthew L Baker; Joanita Jakana; Peter R Weigele; Jonathan King; Wah Chiu
Journal: Nature Date: 2008-02-28 Impact factor: 49.962

5. Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins.

Authors: Stefanie Reissmann; Charles Parnot; Christopher R Booth; Wah Chiu; Judith Frydman
Journal: Nat Struct Mol Biol Date: 2007-04-29 Impact factor: 15.369

6. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

Authors: Xing Zhang; Ethan Settembre; Chen Xu; Philip R Dormitzer; Richard Bellamy; Stephen C Harrison; Nikolaus Grigorieff
Journal: Proc Natl Acad Sci U S A Date: 2008-01-31 Impact factor: 11.205

7. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.

Authors: Xiangan Liu; Wen Jiang; Joanita Jakana; Wah Chiu
Journal: J Struct Biol Date: 2007-07-06 Impact factor: 2.867

8. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

Authors: Sjors H W Scheres; Haixiao Gao; Mikel Valle; Gabor T Herman; Paul P B Eggermont; Joachim Frank; Jose-Maria Carazo
Journal: Nat Methods Date: 2006-12-10 Impact factor: 28.547

9. 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.

Authors: Xuekui Yu; Lei Jin; Z Hong Zhou
Journal: Nature Date: 2008-04-30 Impact factor: 49.962

10. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections.

Authors: Nadav Elad; Daniel K Clare; Helen R Saibil; Elena V Orlova
Journal: J Struct Biol Date: 2007-11-22 Impact factor: 2.867

31 in total

JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.

1. Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope.

2. Modular software platform for low-dose electron microscopy and tomography.

3. De novo backbone trace of GroEL from single particle electron cryomicroscopy.

4. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.

5. Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins.

6. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

7. Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.

8. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

9. 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.

10. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections.

1. Retrofit implementation of Zernike phase plate imaging for cryo-TEM.

2. Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.

3. Automated specimen search in cryo-TEM observation with DIFF-defocus imaging.

Review 4. Automated data collection in single particle electron microscopy.

5. Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency.

6. Genetic analysis of structural proteins in the adsorption apparatus of bacteriophage epsilon 15.

7. CTER-rapid estimation of CTF parameters with error assessment.

Review 8. Determination of the ribosome structure to a resolution of 2.5 Å by single-particle cryo-EM.

9. MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.

10. 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera.