دورية أكاديمية
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin
| العنوان: | Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin |
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| المؤلفون: | Pavel Afanasyev, Charlotte Seer-Linnemayr, Raimond B. G. Ravelli, Rishi Matadeen, Sacha De Carlo, Bart Alewijnse, Rodrigo V. Portugal, Navraj S. Pannu, Michael Schatz, Marin van Heel |
| المصدر: | IUCrJ, Vol 4, Iss 5, Pp 678-694 (2017) |
| بيانات النشر: | International Union of Crystallography, 2017. |
| سنة النشر: | 2017 |
| المجموعة: | LCC:Crystallography |
| مصطلحات موضوعية: | alignment by classification, angular reconstitution, MSA, worm haemoglobin, cryo-EM, Crystallography, QD901-999 |
| الوصف: | Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the `Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (`four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, `random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external `starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive `ABC-4D' pipeline is based on the two-dimensional reference-free `alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2052-2525 20522525 |
| Relation: | http://scripts.iucr.org/cgi-bin/paper?S2052252517010922; https://doaj.org/toc/2052-2525 |
| DOI: | 10.1107/S2052252517010922 |
| URL الوصول: | https://doaj.org/article/84b5977dcdf0496880072bec08d4db4e |
| رقم الأكسشن: | edsdoj.84b5977dcdf0496880072bec08d4db4e |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 20522525 |
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| DOI: | 10.1107/S2052252517010922 |